library(UpSetR)
library(RNASeqBulkExploratory)
library(ggplot2)
library(DESeq2)
library(dplyr)
library(ggvenn)
## Loading required package: scales
## 
## Attaching package: 'scales'
## The following object is masked from 'package:viridis':
## 
##     viridis_pal
library(gplots)
## 
## Attaching package: 'gplots'
## The following object is masked from 'package:IRanges':
## 
##     space
## The following object is masked from 'package:S4Vectors':
## 
##     space
## The following object is masked from 'package:stats':
## 
##     lowess

1. Environment Set Up

for (i in 1:length(params))
  print(paste('Parameter:', names(params)[i], ' - Value:', params[[i]], '- Class:', class(params[[i]])))
## [1] "Parameter: Dataset  - Value: CHD2_iPSCs_and_organoids_PublicRepo - Class: character"
## [1] "Parameter: InputFolder  - Value: /group/testa/Project/CHD2/BulkRNAseq/results/PublicRepo/2.DEA/ - Class: character"
## [1] "Parameter: OutputFolder  - Value: /group/testa/Project/CHD2/BulkRNAseq/results/PublicRepo/9.DEGsComparison/ - Class: character"
## [1] "Parameter: FDRthr  - Value: 0.05 - Class: numeric"
## [1] "Parameter: logFCthr  - Value: 1.5 - Class: numeric"
logFCthr <- params$logFCthr
FDRthr <- params$FDRthr

DEGs are thresholded for Overlap Analysis:

FDR threshold: 0.05

LogFC threshold: 1.5

2. Data Upload

DEA for iPSCs

DEAList_ips_HT <- readRDS(paste0(params$InputFolder, 'iPSCs/Output/Savings/ipsc.DEAList_HT.rds'))
DEAList_ips_AR <- readRDS(paste0(params$InputFolder, 'iPSCs/Output/Savings/ipsc.DEAList_AR.rds'))

DEAList_ips_HT
## $dds
## class: DESeqDataSet 
## dim: 16981 9 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(16981): TSPAN6 TNMD ... C8orf44 PDCD6-AHRR
## rowData names(39): Gene EnsGene ... deviance maxCooks
## colnames(9): OLE_001 OLE_002 ... OLE_029 OLE_030
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 16981 rows and 6 columns
##               baseMean log2FoldChange     lfcSE      stat      pvalue        padj
##              <numeric>      <numeric> <numeric> <numeric>   <numeric>   <numeric>
## TSPAN6        1839.212      0.5049494  0.169534  2.978448 2.89712e-03 1.76964e-02
## TNMD            50.023      2.5175864  0.457319  5.505093 3.68973e-08 7.60379e-07
## DPM1           913.160      0.0795911  0.105715  0.752885 4.51519e-01 6.61882e-01
## SCYL3          150.087     -0.0606176  0.197933 -0.306253 7.59412e-01 8.78588e-01
## C1orf112       597.036     -0.1724953  0.200097 -0.862060 3.88655e-01 6.07051e-01
## ...                ...            ...       ...       ...         ...         ...
## FAM106C        3.59606      -2.331598  1.440608 -1.618482 1.05559e-01 2.66579e-01
## DUS4L-BCAP29 123.17497      -0.572171  0.274235 -2.086427 3.69399e-02 1.26569e-01
## ZCCHC14-DT     2.78524      -0.907292  1.352475 -0.670838 5.02323e-01 7.04955e-01
## C8orf44       59.84408      -0.182321  0.324451 -0.561938 5.74159e-01 7.59580e-01
## PDCD6-AHRR    14.92594      20.246746  3.778515  5.358387 8.39684e-08 1.61297e-06
## 
## $HT$DEGs
##              baseMean log2FoldChange      lfcSE       stat       pvalue         padj
## TNMD        50.023016      2.5175864 0.45731947   5.505093 3.689727e-08 7.603792e-07
## ENPP4      120.688084     -0.7240605 0.24421627  -2.964833 3.028472e-03 1.836004e-02
## SEMA3F     981.569865      0.6190299 0.20863088   2.967106 3.006174e-03 1.823789e-02
## CFTR        35.639635     -3.0173557 0.61695253  -4.890742 1.004565e-06 1.598737e-05
## CD99      1160.492056      0.5887600 0.16556063   3.556160 3.763156e-04 3.258652e-03
## HS3ST1       8.109638      2.7762536 0.85194713   3.258716 1.119177e-03 8.090567e-03
## AOC1         3.937746     -4.6357847 1.59275752  -2.910540 3.608046e-03 2.109788e-02
## KLHL13     256.664221     -0.8484196 0.21147493  -4.011916 6.022795e-05 6.452560e-04
## CFLAR      456.007078      0.5958769 0.14735164   4.043911 5.256689e-05 5.714714e-04
## TFPI        72.040033      0.8425149 0.30125966   2.796640 5.163697e-03 2.819445e-02
## MTMR7      237.606177     -0.7251733 0.18958920  -3.824972 1.307871e-04 1.278582e-03
## SARM1      150.728970     -0.9917129 0.22460403  -4.415384 1.008310e-05 1.294189e-04
## HSPB6       14.175341      2.4452045 0.61862535   3.952642 7.729304e-05 8.062120e-04
## TSPOAP1    218.325261     -0.8755312 0.19503823  -4.489024 7.155037e-06 9.484753e-05
## CROT        78.763633     -0.9719655 0.30672682  -3.168831 1.530532e-03 1.052059e-02
## SOX8       310.520774      1.3514849 0.20759357   6.510244 7.502868e-11 2.324931e-09
## CRLF1      523.506223      3.6889380 0.30274769  12.184859 3.742991e-34 9.347020e-32
## MAP3K14    155.019414     -1.1746157 0.24223979  -4.848979 1.240984e-06 1.928726e-05
## TAC1        18.033082     -1.8776176 0.60080309  -3.125180 1.776964e-03 1.187043e-02
## CX3CL1      39.008169     -3.1649608 0.53120505  -5.958077 2.552225e-09 6.317688e-08
## CACNA1G    149.062043      1.3239452 0.22418550   5.905579 3.514097e-09 8.524698e-08
## PROM1     2072.162377      0.7872385 0.15813341   4.978319 6.413893e-07 1.057421e-05
## NOS2        36.755957     -1.7773442 0.45356703  -3.918592 8.906769e-05 9.133203e-04
## DNAH9       15.995602      2.6872842 0.66435580   4.044947 5.233489e-05 5.693138e-04
## TRAPPC6A   371.386712      0.6959821 0.24133312   2.883906 3.927754e-03 2.260156e-02
## RHBDF1     618.713378      0.7729502 0.15308944   5.049010 4.441043e-07 7.511291e-06
## BAIAP3     202.677197      1.0649157 0.20483420   5.198915 2.004548e-07 3.617347e-06
## MYLIP      895.189470      1.0121983 0.13694071   7.391508 1.451730e-13 6.504440e-12
## SYN1       182.102239     -1.3278508 0.21052875  -6.307218 2.840952e-10 7.987121e-09
## JARID2    8224.824306      0.6261954 0.12760213   4.907406 9.228890e-07 1.478451e-05
## CAMK1G      14.681606     -1.6705286 0.63227040  -2.642111 8.239104e-03 4.061197e-02
## DLEC1       22.924327     -1.3220174 0.49967037  -2.645779 8.150304e-03 4.031469e-02
## CYB561     743.938862      0.8790001 0.14295685   6.148709 7.811611e-10 2.053390e-08
## AASS     13696.295658     -1.0911766 0.12640461  -8.632411 6.007203e-18 4.180669e-16
## NFIX         6.488386      4.4228073 1.40238636   3.153772 1.611748e-03 1.094326e-02
## ST3GAL1    181.289712      1.0278185 0.18300596   5.616312 1.950768e-08 4.182574e-07
## MMP25     1265.400734      1.5078652 0.12270101  12.288939 1.038604e-34 2.755707e-32
## REV3L      355.305028     -0.7006671 0.22764692  -3.077868 2.084875e-03 1.355927e-02
## TENM1      218.272449      2.0145807 0.21905667   9.196619 3.693906e-20 3.015684e-18
## PAX7        15.224684      3.0697407 0.67784484   4.528677 5.935401e-06 8.055929e-05
## CD9       2216.110308      1.2701616 0.11392235  11.149363 7.212064e-29 1.200667e-26
## SEMA3G      90.965836     -1.3530119 0.29194892  -4.634413 3.579514e-06 5.056883e-05
## STAB1       18.714620     -3.1847356 0.72317133  -4.403847 1.063481e-05 1.357818e-04
## IDS        836.079003     -0.9520371 0.17369914  -5.480954 4.230374e-08 8.596665e-07
## PRSS3        4.067363     -5.1203416 1.55386502  -3.295229 9.834139e-04 7.279577e-03
## CD4        102.129267     -0.8295457 0.30406343  -2.728199 6.368111e-03 3.308962e-02
## FYN       1036.538766     -0.7137789 0.17228511  -4.143010 3.427770e-05 3.903338e-04
## MRC2       883.198304      0.9174997 0.13363935   6.865491 6.626316e-12 2.383930e-10
## TSPAN9     908.111816      0.6230343 0.15371935   4.053064 5.055126e-05 5.506164e-04
## PLAUR      169.478993      1.1892446 0.20893456   5.691948 1.255982e-08 2.809992e-07
## MAN2B2     237.658159      0.8106847 0.22195737   3.652434 2.597663e-04 2.354794e-03
## SLC7A14     14.537574     -2.0787110 0.72604902  -2.863045 4.195910e-03 2.386160e-02
## CLDN11      85.160769      1.2571120 0.29574130   4.250715 2.130892e-05 2.528628e-04
## DPEP1      408.259255     -3.3589338 0.26362093 -12.741529 3.475144e-37 1.092804e-34
## IL20RA      45.434941     -0.9372377 0.31773033  -2.949790 3.179903e-03 1.910079e-02
## ATP1A2    1254.559680     -1.9984784 0.20292121  -9.848543 6.954444e-23 7.380838e-21
## ZNF582      91.316247     -1.1544838 0.27761270  -4.158613 3.201856e-05 3.683653e-04
## SYT13      371.170624     -0.8854705 0.18597067  -4.761345 1.923068e-06 2.874614e-05
## CD74       514.416139     -1.2949383 0.23089421  -5.608362 2.042505e-08 4.362739e-07
## ADGRA2     172.234754      2.9760245 0.20737916  14.350644 1.055530e-46 7.468314e-44
## RUNX3       13.116324      1.8545069 0.72026182   2.574768 1.003074e-02 4.719646e-02
## PLEKHB1    254.938718     -2.1675004 0.25734320  -8.422606 3.682008e-17 2.368340e-15
## OSBPL5     246.312599      0.9031717 0.28000578   3.225547 1.257323e-03 8.892377e-03
## CPS1       559.102986     -2.0546093 0.18018758 -11.402614 4.057518e-30 7.177158e-28
## FHL1       708.258743     -0.8951035 0.16578221  -5.399273 6.691133e-08 1.310520e-06
## GRAMD1B    533.862445     -0.8441858 0.27052746  -3.120518 1.805333e-03 1.201324e-02
## DEF6       175.979327      0.7777296 0.27820873   2.795489 5.182119e-03 2.826777e-02
## EHD2       303.678788     -1.2919955 0.22067584  -5.854721 4.778116e-09 1.136375e-07
## RRAGD      415.127177      0.6233723 0.22668537   2.749945 5.960525e-03 3.149212e-02
## VIM        940.982385     -1.6294965 0.19164618  -8.502630 1.853437e-17 1.205870e-15
## FAS         56.880016     -2.6852826 0.47405773  -5.664463 1.474855e-08 3.231550e-07
## RNASET2    401.405612      0.6548899 0.20692002   3.164942 1.551138e-03 1.061663e-02
## CD44        78.713158     -1.1735390 0.27941405  -4.200000 2.669149e-05 3.110832e-04
## KCNG1      460.398241      0.9124319 0.21140631   4.316011 1.588741e-05 1.940893e-04
## BTN3A1     105.847835     -0.9792877 0.34994795  -2.798381 5.135947e-03 2.809714e-02
## PRKCH      215.006991      1.3909029 0.30052789   4.628199 3.688592e-06 5.180809e-05
## HMGB3     8214.937656      0.8097357 0.12578924   6.437241 1.216644e-10 3.637295e-09
## ARHGAP31   224.278647      2.2802469 0.26549779   8.588572 8.805698e-18 5.957353e-16
## APBA2      504.735180      0.6669969 0.13912039   4.794386 1.631735e-06 2.485067e-05
## TMSB10    7559.539981      1.0077127 0.15262170   6.602683 4.037818e-11 1.308515e-09
## DAPK2       34.573991     -1.3991118 0.47744349  -2.930424 3.385000e-03 2.006307e-02
## TIMP2     1179.047488      0.8555700 0.12695661   6.739074 1.593987e-11 5.512727e-10
## FLT4       311.776760      0.9237841 0.16356828   5.647698 1.626109e-08 3.540124e-07
## CDH1      7945.148949      0.6162606 0.14451441   4.264354 2.004816e-05 2.395133e-04
## DNAH5       16.705341     -1.8809808 0.59406870  -3.166268 1.544084e-03 1.059055e-02
## BEST2       41.914040     -1.5060966 0.43539420  -3.459156 5.418703e-04 4.428056e-03
## TNC        112.108829     -1.5243894 0.29838959  -5.108722 3.243453e-07 5.625850e-06
## CAPG       996.645533      0.9123606 0.24102520   3.785333 1.535030e-04 1.480201e-03
## GPM6B     1903.253264      0.6389611 0.13186365   4.845620 1.262171e-06 1.957345e-05
## ATP6V1H    753.543534      0.8202377 0.11230985   7.303347 2.806971e-13 1.215948e-11
## ARAP2       80.240829     -1.7003170 0.36602715  -4.645330 3.395328e-06 4.820742e-05
## FAM184B     11.472343     -2.6472198 0.79208111  -3.342107 8.314501e-04 6.374200e-03
## LMO3       514.967724      2.1902717 0.18955301  11.554930 6.970465e-31 1.345062e-28
## COL9A2     121.556929      1.5708096 0.31712809   4.953234 7.299021e-07 1.189488e-05
## PER3       306.465233     -0.9975477 0.20848832  -4.784669 1.712690e-06 2.588002e-05
## EPN3       128.113525      1.9294358 0.22399709   8.613665 7.076154e-18 4.845168e-16
## LTBP1     1496.357212      0.7230251 0.13491544   5.359098 8.363839e-08 1.608452e-06
## PPP1R3F    171.272506     -0.6425219 0.21362207  -3.007750 2.631891e-03 1.641886e-02
## NEXMIF      29.754512     -1.4492828 0.52030062  -2.785472 5.344987e-03 2.894235e-02
## LAMC3     1465.199421      1.6712541 0.20942703   7.980126 1.461838e-15 8.007570e-14
## COL23A1    491.493590      1.0759317 0.25902141   4.153833 3.269518e-05 3.741219e-04
## HERPUD1    427.813849      0.6633018 0.16113945   4.116322 3.849671e-05 4.320639e-04
## HOMER3     469.067082      0.7202037 0.23718701   3.036438 2.393913e-03 1.514569e-02
## PRSS8     2016.894882      0.6840759 0.19474061   3.512754 4.434874e-04 3.750428e-03
## FSTL4       80.135907     -0.7450135 0.28725481  -2.593563 9.498704e-03 4.530323e-02
## NNAT       765.967350      2.2007744 0.14728942  14.941836 1.760565e-50 1.660898e-47
## ENTPD2      81.875793      0.9002594 0.29444422   3.057487 2.232013e-03 1.431534e-02
## LY75        65.271233     -1.4927578 0.43928733  -3.398135 6.784686e-04 5.351173e-03
## SDCCAG8    153.028843      0.9812737 0.24752960   3.964268 7.362152e-05 7.711969e-04
## FOXC1      162.492186      7.7712273 1.12352274   6.916840 4.618282e-12 1.693802e-10
## SYNE2     3649.954266      0.9123672 0.15151617   6.021583 1.727194e-09 4.332273e-08
## ATP9A      557.565064     -0.8385044 0.24114155  -3.477229 5.066251e-04 4.180273e-03
## KCNH2      330.101458      1.0610931 0.30149366   3.519454 4.324362e-04 3.678957e-03
## EIF2AK2   2561.318175     -0.8191185 0.15898472  -5.152183 2.574710e-07 4.535388e-06
## NPFFR2      58.683708      1.9178066 0.38161934   5.025444 5.022691e-07 8.436233e-06
## TRAF3IP2   483.881342      1.0727380 0.15980331   6.712864 1.908405e-11 6.533594e-10
## SERPINB3    30.828152     -8.2133249 1.34765345  -6.094538 1.097541e-09 2.819567e-08
## F7          13.880892     -2.1693636 0.80534589  -2.693704 7.066285e-03 3.599058e-02
## CDK14     1098.121727      1.1000754 0.13823453   7.958036 1.747912e-15 9.513237e-14
## PTPRU     1508.517016      0.6902236 0.16314326   4.230782 2.328798e-05 2.740554e-04
## RIMBP2      31.504709      2.2750683 0.40056856   5.679598 1.350118e-08 2.995360e-07
## GUCY1B1    118.008038      2.6523076 0.34604769   7.664573 1.794277e-14 8.831485e-13
## TNK2      1065.177832      0.6025731 0.19017914   3.168450 1.532540e-03 1.052059e-02
## DGAT2       61.567664     -1.4337723 0.39095898  -3.667322 2.451045e-04 2.237698e-03
## SEZ6        62.433943     -2.6235166 0.44921196  -5.840264 5.211806e-09 1.236057e-07
## CA11      1157.331236     -0.9119232 0.24159745  -3.774556 1.602927e-04 1.538969e-03
## TM7SF3    1459.830219     -0.7387118 0.09760295  -7.568540 3.774432e-14 1.795340e-12
## DLX3         9.322955      2.8108034 0.83252168   3.376252 7.348045e-04 5.734244e-03
## ATP2C2      55.201458      1.0992590 0.38481431   2.856596 4.282104e-03 2.426240e-02
## NGFR       156.818745      1.1198266 0.23733247   4.718387 2.377214e-06 3.476957e-05
## SLC12A2    378.045680     -0.6870590 0.24745010  -2.776556 5.493822e-03 2.955584e-02
## CALCRL      47.728614     -1.5349437 0.37008883  -4.147501 3.361245e-05 3.835841e-04
## OAT       2009.440607      1.3344562 0.13805208   9.666324 4.191647e-22 4.162477e-20
## NTN1        96.163904      0.9315215 0.32288935   2.884956 3.914685e-03 2.254163e-02
## SNAP91      22.910533     -1.5123603 0.55544964  -2.722768 6.473756e-03 3.353595e-02
## COL17A1     39.792053     -1.4127033 0.40004673  -3.531346 4.134512e-04 3.531597e-03
## TLE2       200.372276      2.2458430 0.33048238   6.795651 1.078244e-11 3.822475e-10
## FAM107B    662.747739      0.8711286 0.13624045   6.394052 1.615461e-10 4.721540e-09
## ME1        227.388590     -0.7693135 0.16806421  -4.577498 4.705712e-06 6.512444e-05
## CTNNA2     132.018902     -0.9224598 0.23081534  -3.996527 6.427847e-05 6.817694e-04
## TIE1        58.637160     -1.2862725 0.40335398  -3.188942 1.427944e-03 9.929533e-03
## MPPED2      44.686786     -1.0783944 0.33613577  -3.208211 1.335636e-03 9.360478e-03
## FECH       620.166821     -0.7193559 0.14995302  -4.797209 1.608918e-06 2.452517e-05
## PFKP      2332.396435     -0.6026955 0.13009963  -4.632568 3.611569e-06 5.093692e-05
## PHKA1      373.951019      0.6072118 0.17885549   3.394985 6.863229e-04 5.398077e-03
## PDK3      1386.343233      0.6890946 0.10612045   6.493513 8.385737e-11 2.573030e-09
## PYGM       134.330454     -0.6875300 0.24184695  -2.842831 4.471475e-03 2.505945e-02
## SDK2       731.209823      1.5152087 0.28630525   5.292284 1.207981e-07 2.266600e-06
## BCL3        47.387774      1.7422493 0.42178052   4.130701 3.616582e-05 4.088760e-04
## MAOB        48.593603     -1.0612869 0.31928356  -3.323964 8.874777e-04 6.694918e-03
## PIGB       104.420622     -0.6796502 0.22587102  -3.009019 2.620928e-03 1.636851e-02
## RAB27A     169.597782     -0.6133747 0.21809805  -2.812381 4.917627e-03 2.705093e-02
## NUCB2      345.511309     -0.8853450 0.15884301  -5.573711 2.493694e-08 5.293177e-07
## WIPI1      295.583513      1.1593150 0.23906766   4.849317 1.238871e-06 1.928255e-05
## ASNS      4133.305247      1.0099430 0.36793335   2.744907 6.052797e-03 3.184844e-02
## PTPN21     531.666906     -0.9236141 0.16752265  -5.513368 3.520304e-08 7.316803e-07
## OSBPL3     475.275198      0.8563552 0.17561902   4.876210 1.081435e-06 1.708264e-05
## NCK2      1705.958584      0.5850421 0.14355708   4.075328 4.594958e-05 5.079882e-04
## RPS6KA2    783.616890      0.9986531 0.15465240   6.457404 1.065142e-10 3.218360e-09
## TRIB2     1516.829531      0.9360330 0.14024578   6.674233 2.485283e-11 8.394336e-10
## LIMS2       45.633961     -1.6630993 0.41605130  -3.997342 6.405772e-05 6.801176e-04
## SREBF1    2410.892025      0.6313895 0.15737315   4.012054 6.019277e-05 6.452560e-04
## TRNT1      416.582301     -0.8270990 0.17294398  -4.782468 1.731561e-06 2.611335e-05
## ACAP1      328.109251     -1.0651817 0.21833566  -4.878643 1.068182e-06 1.688902e-05
## CRMP1     2921.222256      1.3845083 0.11824580  11.708732 1.149869e-31 2.352520e-29
## ADAM11     130.541352     -0.5928451 0.20330697  -2.916010 3.545392e-03 2.081753e-02
##  [ reached 'max' / getOption("max.print") -- omitted 2408 rows ]
## 
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 16981 rows and 5 columns
##               baseMean log2FoldChange     lfcSE      pvalue        padj
##              <numeric>      <numeric> <numeric>   <numeric>   <numeric>
## TSPAN6        1839.212      0.3601871 0.1780761 2.89712e-03 1.76964e-02
## TNMD            50.023      2.2521088 0.4685196 3.68973e-08 7.60379e-07
## DPM1           913.160      0.0598697 0.0919778 4.51519e-01 6.61882e-01
## SCYL3          150.087     -0.0301068 0.1398662 7.59412e-01 8.78588e-01
## C1orf112       597.036     -0.0865917 0.1450572 3.88655e-01 6.07051e-01
## ...                ...            ...       ...         ...         ...
## FAM106C        3.59606      -0.299826  0.690995 1.05559e-01 2.66579e-01
## DUS4L-BCAP29 123.17497      -0.287169  0.252811 3.69399e-02 1.26569e-01
## ZCCHC14-DT     2.78524      -0.091265  0.454908 5.02323e-01 7.04955e-01
## C8orf44       59.84408      -0.059125  0.189225 5.74159e-01 7.59580e-01
## PDCD6-AHRR    14.92594      12.530118  3.449307 8.39684e-08 1.61297e-06
## 
## $HT$DEGsAshr
##               baseMean log2FoldChange     lfcSE       pvalue         padj
## TNMD         50.023016      2.2521088 0.4685196 3.689727e-08 7.603792e-07
## CFTR         35.639635     -2.5732161 0.6584404 1.004565e-06 1.598737e-05
## HS3ST1        8.109638      1.6071214 1.0290554 1.119177e-03 8.090567e-03
## AOC1          3.937746     -1.3855103 1.6906527 3.608046e-03 2.109788e-02
## KLHL13      256.664221     -0.7432323 0.2449716 6.022795e-05 6.452560e-04
## MTMR7       237.606177     -0.6113749 0.2234354 1.307871e-04 1.278582e-03
## SARM1       150.728970     -0.9053621 0.2443980 1.008310e-05 1.294189e-04
## HSPB6        14.175341      1.9061709 0.6849187 7.729304e-05 8.062120e-04
## TSPOAP1     218.325261     -0.8015765 0.2158768 7.155037e-06 9.484753e-05
## CROT         78.763633     -0.7206616 0.3731804 1.530532e-03 1.052059e-02
## SOX8        310.520774      1.2927871 0.2070244 7.502868e-11 2.324931e-09
## CRLF1       523.506223      3.6182315 0.3087240 3.742991e-34 9.347020e-32
## MAP3K14     155.019414     -1.0905843 0.2490714 1.240984e-06 1.928726e-05
## TAC1         18.033082     -1.1978268 0.7166493 1.776964e-03 1.187043e-02
## CX3CL1       39.008169     -2.8603633 0.5601812 2.552225e-09 6.317688e-08
## CACNA1G     149.062043      1.2555713 0.2239040 3.514097e-09 8.524698e-08
## PROM1      2072.162377      0.7356813 0.1727412 6.413893e-07 1.057421e-05
## NOS2         36.755957     -1.4644857 0.4938284 8.906769e-05 9.133203e-04
## DNAH9        15.995602      2.0940670 0.7382690 5.233489e-05 5.693138e-04
## RHBDF1      618.713378      0.7235989 0.1671261 4.441043e-07 7.511291e-06
## BAIAP3      202.677197      1.0053635 0.2099293 2.004548e-07 3.617347e-06
## MYLIP       895.189470      0.9877661 0.1370771 1.451730e-13 6.504440e-12
## SYN1        182.102239     -1.2676126 0.2099951 2.840952e-10 7.987121e-09
## CAMK1G       14.681606     -0.8220175 0.7032247 8.239104e-03 4.061197e-02
## DLEC1        22.924327     -0.7223058 0.5719810 8.150304e-03 4.031469e-02
## CYB561      743.938862      0.8491047 0.1467250 7.811611e-10 2.053390e-08
## AASS      13696.295658     -1.0702605 0.1261122 6.007203e-18 4.180669e-16
## NFIX          6.488386      1.8136722 1.7173830 1.611748e-03 1.094326e-02
## ST3GAL1     181.289712      0.9814334 0.1860950 1.950768e-08 4.182574e-07
## MMP25      1265.400734      1.4869531 0.1226916 1.038604e-34 2.755707e-32
## TENM1       218.272449      1.9500646 0.2198154 3.693906e-20 3.015684e-18
## PAX7         15.224684      2.5261506 0.7396790 5.935401e-06 8.055929e-05
## CD9        2216.110308      1.2524610 0.1137531 7.212064e-29 1.200667e-26
## SEMA3G       90.965836     -1.2312132 0.2998878 3.579514e-06 5.056883e-05
## STAB1        18.714620     -2.5725913 0.8045609 1.063481e-05 1.357818e-04
## IDS         836.079003     -0.9079732 0.1791343 4.230374e-08 8.596665e-07
## PRSS3         4.067363     -2.2295021 2.0253663 9.834139e-04 7.279577e-03
## FYN        1036.538766     -0.6242334 0.1997312 3.427770e-05 3.903338e-04
## MRC2        883.198304      0.8933721 0.1351033 6.626316e-12 2.383930e-10
## PLAUR       169.478993      1.1300722 0.2096937 1.255982e-08 2.809992e-07
## MAN2B2      237.658159      0.6721013 0.2647263 2.597663e-04 2.354794e-03
## SLC7A14      14.537574     -1.0732431 0.8342941 4.195910e-03 2.386160e-02
## CLDN11       85.160769      1.1220588 0.3153850 2.130892e-05 2.528628e-04
## DPEP1       408.259255     -3.2954297 0.2679488 3.475144e-37 1.092804e-34
## IL20RA       45.434941     -0.6429320 0.3828441 3.179903e-03 1.910079e-02
## ATP1A2     1254.559680     -1.9430461 0.2035211 6.954444e-23 7.380838e-21
## ZNF582       91.316247     -1.0279645 0.3023202 3.201856e-05 3.683653e-04
## SYT13       371.170624     -0.8237021 0.2013247 1.923068e-06 2.874614e-05
## CD74        514.416139     -1.2222721 0.2312085 2.042505e-08 4.362739e-07
## ADGRA2      172.234754      2.9295759 0.2092814 1.055530e-46 7.468314e-44
## RUNX3        13.116324      0.8132997 0.7664458 1.003074e-02 4.719646e-02
## PLEKHB1     254.938718     -2.0799439 0.2588130 3.682008e-17 2.368340e-15
## OSBPL5      246.312599      0.6822974 0.3400291 1.257323e-03 8.892377e-03
## CPS1        559.102986     -2.0112063 0.1806459 4.057518e-30 7.177158e-28
## FHL1        708.258743     -0.8521347 0.1732540 6.691133e-08 1.310520e-06
## GRAMD1B     533.862445     -0.6173684 0.3266069 1.805333e-03 1.201324e-02
## EHD2        303.678788     -1.2258576 0.2205391 4.778116e-09 1.136375e-07
## VIM         940.982385     -1.5787570 0.1917393 1.853437e-17 1.205870e-15
## FAS          56.880016     -2.4091201 0.4888209 1.474855e-08 3.231550e-07
## CD44         78.713158     -1.0478735 0.3021954 2.669149e-05 3.110832e-04
## KCNG1       460.398241      0.8261015 0.2356891 1.588741e-05 1.940893e-04
## BTN3A1      105.847835     -0.6259525 0.4154034 5.135947e-03 2.809714e-02
## PRKCH       215.006991      1.2622131 0.3082738 3.688592e-06 5.180809e-05
## HMGB3      8214.937656      0.7846510 0.1299879 1.216644e-10 3.637295e-09
## ARHGAP31    224.278647      2.1884948 0.2673574 8.805698e-18 5.957353e-16
## APBA2       504.735180      0.6083904 0.1561810 1.631735e-06 2.485067e-05
## TMSB10     7559.539981      0.9768376 0.1533985 4.037818e-11 1.308515e-09
## DAPK2        34.573991     -0.8895045 0.5722080 3.385000e-03 2.006307e-02
## TIMP2      1179.047488      0.8323932 0.1295492 1.593987e-11 5.512727e-10
## FLT4        311.776760      0.8845133 0.1686246 1.626109e-08 3.540124e-07
## DNAH5        16.705341     -1.2241736 0.7086132 1.544084e-03 1.059055e-02
## BEST2        41.914040     -1.1605079 0.5090819 5.418703e-04 4.428056e-03
## TNC         112.108829     -1.4014187 0.3000735 3.243453e-07 5.625850e-06
## CAPG        996.645533      0.7784483 0.2828417 1.535030e-04 1.480201e-03
## ATP6V1H     753.543534      0.8018084 0.1144714 2.806971e-13 1.215948e-11
## ARAP2        80.240829     -1.5132036 0.3731216 3.395328e-06 4.820742e-05
## FAM184B      11.472343     -1.6414593 0.9534324 8.314501e-04 6.374200e-03
## LMO3        514.967724      2.1430498 0.1901748 6.970465e-31 1.345062e-28
## COL9A2      121.556929      1.4314405 0.3199455 7.299021e-07 1.189488e-05
## PER3        306.465233     -0.9295161 0.2203057 1.712690e-06 2.588002e-05
## EPN3        128.113525      1.8613948 0.2246919 7.076154e-18 4.845168e-16
## LTBP1      1496.357212      0.6812595 0.1466951 8.363839e-08 1.608452e-06
## NEXMIF       29.754512     -0.8384240 0.6100941 5.344987e-03 2.894235e-02
## LAMC3      1465.199421      1.6107888 0.2096012 1.461838e-15 8.007570e-14
## COL23A1     491.493590      0.9604675 0.2852627 3.269518e-05 3.741219e-04
## NNAT        765.967350      2.1723463 0.1475860 1.760565e-50 1.660898e-47
## ENTPD2       81.875793      0.6442738 0.3563482 2.232013e-03 1.431534e-02
## LY75         65.271233     -1.1319991 0.5177355 6.784686e-04 5.351173e-03
## SDCCAG8     153.028843      0.8593494 0.2825371 7.362152e-05 7.711969e-04
## FOXC1       162.492186      7.2748157 1.1348759 4.618282e-12 1.693802e-10
## SYNE2      3649.954266      0.8795419 0.1550761 1.727194e-09 4.332273e-08
## ATP9A       557.565064     -0.6734277 0.2902653 5.066251e-04 4.180273e-03
## KCNH2       330.101458      0.8627737 0.3583607 4.324362e-04 3.678957e-03
## EIF2AK2    2561.318175     -0.7723027 0.1708352 2.574710e-07 4.535388e-06
## NPFFR2       58.683708      1.7193603 0.3856310 5.022691e-07 8.436233e-06
## TRAF3IP2    483.881342      1.0390289 0.1599288 1.908405e-11 6.533594e-10
## SERPINB3     30.828152     -7.4918317 1.3667030 1.097541e-09 2.819567e-08
## F7           13.880892     -0.9511046 0.8714615 7.066285e-03 3.599058e-02
## CDK14      1098.121727      1.0749909 0.1379182 1.747912e-15 9.513237e-14
## PTPRU      1508.517016      0.6065077 0.1881633 2.328798e-05 2.740554e-04
## RIMBP2       31.504709      2.0644763 0.4062017 1.350118e-08 2.995360e-07
## GUCY1B1     118.008038      2.5064949 0.3521884 1.794277e-14 8.831485e-13
## DGAT2        61.567664     -1.1696497 0.4448005 2.451045e-04 2.237698e-03
## SEZ6         62.433943     -2.3730113 0.4611791 5.211806e-09 1.236057e-07
## CA11       1157.331236     -0.7767772 0.2838137 1.602927e-04 1.538969e-03
## TM7SF3     1459.830219     -0.7222063 0.1004903 3.774432e-14 1.795340e-12
## DLX3          9.322955      1.7308352 1.0090067 7.348045e-04 5.734244e-03
## ATP2C2       55.201458      0.7104228 0.4613474 4.282104e-03 2.426240e-02
## NGFR        156.818745      1.0364491 0.2472759 2.377214e-06 3.476957e-05
## CALCRL       47.728614     -1.3300169 0.3927711 3.361245e-05 3.835841e-04
## OAT        2009.440607      1.3083110 0.1378280 4.191647e-22 4.162477e-20
## NTN1         96.163904      0.6223985 0.3865091 3.914685e-03 2.254163e-02
## SNAP91       22.910533     -0.8263346 0.6401815 6.473756e-03 3.353595e-02
## COL17A1      39.792053     -1.1210586 0.4646038 4.134512e-04 3.531597e-03
## TLE2        200.372276      2.1024677 0.3337216 1.078244e-11 3.822475e-10
## FAM107B     662.747739      0.8442795 0.1393908 1.615461e-10 4.721540e-09
## ME1         227.388590     -0.7026279 0.1887658 4.705712e-06 6.512444e-05
## CTNNA2      132.018902     -0.8099654 0.2649293 6.427847e-05 6.817694e-04
## TIE1         58.637160     -0.9342005 0.4870382 1.427944e-03 9.929533e-03
## MPPED2       44.686786     -0.8053188 0.4082660 1.335636e-03 9.360478e-03
## FECH        620.166821     -0.6614984 0.1675619 1.608918e-06 2.452517e-05
## PDK3       1386.343233      0.6639277 0.1121757 8.385737e-11 2.573030e-09
## SDK2        731.209823      1.4023777 0.2871150 1.207981e-07 2.266600e-06
## BCL3         47.387774      1.4812960 0.4470573 3.616582e-05 4.088760e-04
## MAOB         48.593603     -0.8218037 0.3858224 8.874777e-04 6.694918e-03
## NUCB2       345.511309     -0.8463582 0.1652897 2.493694e-08 5.293177e-07
## WIPI1       295.583513      1.0771951 0.2461660 1.238871e-06 1.928255e-05
## ASNS       4133.305247      0.6259185 0.4334900 6.052797e-03 3.184844e-02
## PTPN21      531.666906     -0.8817621 0.1734212 3.520304e-08 7.316803e-07
## OSBPL3      475.275198      0.8000578 0.1899663 1.081435e-06 1.708264e-05
## RPS6KA2     783.616890      0.9667465 0.1557352 1.065142e-10 3.218360e-09
## TRIB2      1516.829531      0.9094918 0.1417579 2.485283e-11 8.394336e-10
## LIMS2        45.633961     -1.4007193 0.4484357 6.405772e-05 6.801176e-04
## TRNT1       416.582301     -0.7681388 0.1894316 1.731561e-06 2.611335e-05
## ACAP1       328.109251     -0.9947591 0.2269858 1.068182e-06 1.688902e-05
## CRMP1      2921.222256      1.3651798 0.1181540 1.149869e-31 2.352520e-29
## MAP3K13      86.469668     -5.8181731 0.7169905 1.748234e-17 1.146207e-15
## FRY         232.964767     -0.9316545 0.2464346 8.304650e-06 1.084779e-04
## PPP2R2C     266.194600      0.8818560 0.1983447 5.971592e-07 9.931793e-06
## ATP2A3      621.823576      0.9641604 0.2064955 3.071384e-07 5.343768e-06
## MGLL         25.276589      1.3829390 0.5570557 2.862851e-04 2.562681e-03
## LMAN1      2830.324995     -0.7947970 0.1000126 2.442038e-16 1.444887e-14
## KCNQ2       916.675310      1.0037192 0.1958389 4.237329e-08 8.596665e-07
## SEMA3C       53.015364      1.9813179 0.4246295 1.228791e-07 2.303101e-06
## GRAMD4      597.976839      0.8667563 0.2080881 1.714588e-06 2.588038e-05
## WNT8B         7.904379     -0.8873774 0.9075553 9.316804e-03 4.462868e-02
## FGF4         26.729090      3.3405509 0.5940399 8.394433e-11 2.573030e-09
## VPS9D1      104.798549      0.6682933 0.3601042 1.924849e-03 1.266894e-02
## ZNF37A       96.568800      4.5962140 1.1429425 3.051023e-07 5.319243e-06
## CACNG4       96.026048      0.8182299 0.4080936 1.224481e-03 8.707250e-03
## FSCN1      8776.866763      1.3715161 0.1393231 1.169512e-23 1.298005e-21
## TRAF4      3239.456673      0.5994841 0.1514121 1.209375e-06 1.884601e-05
## MCAM        469.858295      0.6366113 0.2658753 3.993115e-04 3.428063e-03
## IL4R        824.302440      0.7814571 0.2186518 1.091034e-05 1.384667e-04
## CAPN6       164.928131     -1.8751738 0.2340373 6.514863e-17 4.127944e-15
## NAALAD2     135.711789      1.0840915 0.2181812 9.863393e-08 1.871400e-06
## FBLN1      3061.849265      1.1498920 0.1276414 5.354839e-20 4.269039e-18
## NEBL        554.440907     -1.7165868 0.2408979 7.984745e-14 3.684483e-12
## ADCYAP1R1   363.989423     -0.8566939 0.1791412 1.271222e-07 2.369552e-06
## ITM2A       367.678214      1.0652218 0.1758327 2.944624e-10 8.264901e-09
## RUNX1T1     612.563495      0.7176010 0.1474016 3.694338e-08 7.604068e-07
## SLC1A3      759.140840      1.7123797 0.2049705 5.167360e-18 3.610985e-16
## FDFT1     10031.670273      0.6756250 0.1084655 1.415770e-11 4.916399e-10
## RIMS1        23.639614     -1.1750029 0.6621264 1.510776e-03 1.041538e-02
## MOXD1        92.085937     -1.2896019 0.2856183 7.113602e-07 1.162706e-05
## EPHA6        22.587819     -1.3951057 0.6152575 4.399298e-04 3.731492e-03
## SMARCA2     252.357350      1.0951221 0.2881547 9.829702e-06 1.263574e-04
## COL5A3       40.088982     -0.8621464 0.4906283 2.194378e-03 1.413609e-02
## CHRNA3       74.627518      2.3268584 0.3323636 6.030563e-14 2.813324e-12
## AFP          15.059954     -0.8129344 0.6881552 8.198269e-03 4.047875e-02
## MEF2C        18.573701      1.0326362 0.6508619 2.632862e-03 1.641888e-02
## CDC14B     2208.141077      1.1481881 0.1300931 2.787200e-19 2.057802e-17
## LRP2         58.041498     -0.8880912 0.4977485 2.016842e-03 1.316724e-02
## AACS       1206.364698      1.3215611 0.1025454 9.579459e-39 3.536278e-36
## PCDHA6       85.700980      5.0434833 0.4824361 4.504472e-27 6.769065e-25
## ATP8B1      174.449562      1.5698899 0.1897492 1.354941e-17 8.987598e-16
## IL12RB2      44.227342     -3.0114888 0.6295984 1.080735e-08 2.450196e-07
## SMARCD3      92.988690      1.2204619 0.2532877 1.981666e-07 3.579858e-06
## SERTAD4      97.634658      1.5922135 0.2560925 4.924238e-11 1.574736e-09
## GRHL2       966.401906      0.6661774 0.1346183 1.725766e-08 3.733150e-07
## P2RX5        77.942447     -1.3249567 0.3583354 1.349016e-05 1.678296e-04
## MECOM        95.586553      5.4399266 0.4693840 2.031519e-32 4.480160e-30
## TTC39A      110.918760     -1.2037853 0.3051202 6.289077e-06 8.455646e-05
## NME8          8.905710      1.0566152 0.9726193 5.630885e-03 3.006857e-02
## EPDR1       196.187785     -1.3352088 0.1985118 2.925507e-12 1.116360e-10
## SEPHS1    16750.668277      0.6852332 0.1627869 6.011328e-07 9.985157e-06
## FAT2         27.514823     -1.2665840 0.6910246 1.197981e-03 8.553816e-03
## MYBPC2      106.559788     -1.4011539 0.2631847 1.322179e-08 2.942584e-07
## TMPRSS11E    36.946326      2.1960725 0.4308838 9.640259e-09 2.209194e-07
## MMP2       1229.479440      1.4157988 0.1410738 1.544642e-24 1.847153e-22
## TFAP2C      279.948004      2.3208808 0.2641476 3.910778e-20 3.177461e-18
## DOCK3       361.908463     -0.9061087 0.2239924 3.061864e-06 4.398775e-05
## SMOX        184.941602      0.5936619 0.2321203 2.355212e-04 2.160662e-03
## F11          21.600248      1.7798861 0.5085462 1.473781e-05 1.814813e-04
## CHGB         55.167346     -1.3626201 0.3993194 3.056330e-05 3.540215e-04
## TBX5        124.839204      7.7869098 0.6924131 1.019221e-30 1.944651e-28
## GRAMD1A    4155.693890      1.4263305 0.1258104 1.223617e-30 2.283323e-28
## ANKRD24     262.545013     -1.3381464 0.2149976 7.862820e-11 2.423204e-09
## PCBP4       623.901957      1.2180983 0.1908087 3.492537e-11 1.144918e-09
## YPEL3       430.038339      0.6372106 0.1870250 1.248496e-05 1.568099e-04
##  [ reached 'max' / getOption("max.print") -- omitted 1964 rows ]
DEAList_ips_AR
## $dds
## class: DESeqDataSet 
## dim: 16616 6 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(16616): TSPAN6 TNMD ... ZCCHC14-DT C8orf44
## rowData names(35): Gene EnsGene ... deviance maxCooks
## colnames(6): OLE_001 OLE_004 ... OLE_028 OLE_029
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 16616 rows and 6 columns
##               baseMean log2FoldChange     lfcSE       stat    pvalue      padj
##              <numeric>      <numeric> <numeric>  <numeric> <numeric> <numeric>
## TSPAN6        1589.535     -0.0550846  0.174872  -0.315000  0.752761         1
## TNMD            17.887      0.2107732  0.747061   0.282136  0.777839         1
## DPM1           906.561     -0.1257532  0.137613  -0.913819  0.360812         1
## SCYL3          154.222     -0.3003555  0.246447  -1.218744  0.222941         1
## C1orf112       648.142      0.1465394  0.163139   0.898250  0.369052         1
## ...                ...            ...       ...        ...       ...       ...
## DHX9-AS1      29.60314     -0.2629160  0.519740 -0.5058608  0.612954         1
## FAM106C        4.86974     -1.0198905  1.337371 -0.7626087  0.445697         1
## DUS4L-BCAP29 145.46191      0.0188132  0.258039  0.0729083  0.941879         1
## ZCCHC14-DT     3.39608      0.1693334  1.660320  0.1019885  0.918766         1
## C8orf44       65.41901      0.1318853  0.382319  0.3449614  0.730123         1
## 
## $AR$DEGs
##              baseMean log2FoldChange     lfcSE       stat        pvalue          padj
## ZNF506      282.22948     -1.1469872 0.2254824  -5.086816  3.641255e-07  3.559005e-04
## LRRC61      179.67569     -2.0922217 0.3163432  -6.613771  3.746522e-11  5.659291e-08
## TNNI3       132.34495     -1.6007541 0.3222102  -4.968044  6.763179e-07  6.243165e-04
## TFCP2      1310.51190     -0.9328431 0.1343744  -6.942121  3.862550e-12  8.022517e-09
## SLC15A4     115.23229     -5.1079818 0.5294291  -9.648095  5.007748e-22  2.080219e-18
## GLT1D1       35.04699     -8.5371005 1.5188848  -5.620637  1.902544e-08  2.107512e-05
## TMEM132D     28.11173     -8.5505683 1.5561545  -5.494678  3.914233e-08  4.064931e-05
## ZNF667-AS1  168.69830     -1.5483536 0.2713436  -5.706247  1.154944e-08  1.370753e-05
## PDE12       405.03599     -0.8485260 0.1923334  -4.411745  1.025407e-05  8.519085e-03
## TSPYL5      224.24750      1.5349468 0.2340561   6.558029  5.452348e-11  7.549685e-08
## LINC01551    56.26912      6.4736795 1.4578688   4.440509  8.974633e-06  7.848553e-03
## ZNF605      572.95301     -1.2157483 0.1815000  -6.698336  2.108059e-11  3.587438e-08
## ZFP28       130.64609     -1.2366492 0.2956687  -4.182551  2.882569e-05  2.082468e-02
## ZNF100      325.99274     -1.6916313 0.2170362  -7.794236  6.479953e-15  1.794515e-11
## ZNF667      256.97551     -1.5924777 0.2378663  -6.694843  2.159026e-11  3.587438e-08
## INPP5F     1225.87509     -1.7132772 0.1507428 -11.365567  6.206010e-30  5.155953e-26
## LINC00654    20.33855     -3.2974285 0.7662166  -4.303520  1.681058e-05  1.330117e-02
## SMIM11      120.22975     -3.8723953 0.4257387  -9.095710  9.397079e-20  3.122837e-16
## MEG3       5539.22335    -11.1894198 0.5122889 -21.842012 9.258705e-106 1.538426e-101
## MEG9        146.77233    -10.5026446 1.4680881  -7.153961  8.430919e-13  2.001259e-09
## MEG8        128.09806     -4.8573576 0.4586376 -10.590839  3.286326e-26  1.820187e-22
## LINC01515    35.93465     -5.7551523 0.9899801  -5.813402  6.121579e-09  7.824319e-06
## ZNF585B     234.21712     -1.1126851 0.2754908  -4.038919  5.369803e-05  3.692043e-02
## PABPC4L      92.75336     -1.3278578 0.3294148  -4.030960  5.554951e-05  3.692043e-02
## ZNF229       25.89545     -3.4262037 0.8155220  -4.201240  2.654570e-05  2.004924e-02
## 
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 16616 rows and 5 columns
##               baseMean log2FoldChange      lfcSE    pvalue      padj
##              <numeric>      <numeric>  <numeric> <numeric> <numeric>
## TSPAN6        1589.535   -0.000115952 0.00805291  0.752761         1
## TNMD            17.887    0.000125439 0.01870128  0.777839         1
## DPM1           906.561   -0.000417418 0.00810677  0.360812         1
## SCYL3          154.222   -0.000424422 0.01112184  0.222941         1
## C1orf112       648.142    0.000358484 0.00834297  0.369052         1
## ...                ...            ...        ...       ...       ...
## DHX9-AS1      29.60314   -1.71831e-04 0.01425308  0.612954         1
## FAM106C        4.86974   -6.95825e-04 0.04097068  0.445697         1
## DUS4L-BCAP29 145.46191    2.09647e-05 0.00861825  0.941879         1
## ZCCHC14-DT     3.39608    9.31383e-05 0.03906130  0.918766         1
## C8orf44       65.41901    9.66827e-05 0.01060372  0.730123         1
## 
## $AR$DEGsAshr
##              baseMean log2FoldChange     lfcSE        pvalue          padj
## ZNF506      282.22948     -1.1027582 0.2633438  3.641255e-07  3.559005e-04
## LRRC61      179.67569     -2.0245757 0.3160109  3.746522e-11  5.659291e-08
## TNNI3       132.34495     -1.4959925 0.3995629  6.763179e-07  6.243165e-04
## TFCP2      1310.51190     -0.9249087 0.1338903  3.862550e-12  8.022517e-09
## SLC15A4     115.23229     -5.0537930 0.5314937  5.007748e-22  2.080219e-18
## GLT1D1       35.04699     -7.9302563 1.5086247  1.902544e-08  2.107512e-05
## TMEM132D     28.11173     -7.9011221 1.5749680  3.914233e-08  4.064931e-05
## ZNF667-AS1  168.69830     -1.5021003 0.2716018  1.154944e-08  1.370753e-05
## PDE12       405.03599     -0.5874130 0.4123360  1.025407e-05  8.519085e-03
## TSPYL5      224.24750      1.5010568 0.2326347  5.452348e-11  7.549685e-08
## LINC01551    56.26912      4.2113983 2.9979915  8.974633e-06  7.848553e-03
## ZNF605      572.95301     -1.1980383 0.1805340  2.108059e-11  3.587438e-08
## ZFP28       130.64609     -0.6361358 0.6305834  2.882569e-05  2.082468e-02
## ZNF100      325.99274     -1.6609406 0.2161810  6.479953e-15  1.794515e-11
## ZNF667      256.97551     -1.5568135 0.2364974  2.159026e-11  3.587438e-08
## INPP5F     1225.87509     -1.6982290 0.1504768  6.206010e-30  5.155953e-26
## LINC00654    20.33855     -1.8452323 1.5928279  1.681058e-05  1.330117e-02
## SMIM11      120.22975     -3.8137804 0.4342392  9.397079e-20  3.122837e-16
## MEG3       5539.22335    -11.0961889 0.5101502 9.258705e-106 1.538426e-101
## MEG9        146.77233     -9.8246236 1.4200792  8.430919e-13  2.001259e-09
## MEG8        128.09806     -4.8156095 0.4610276  3.286326e-26  1.820187e-22
## LINC01515    35.93465     -5.5465185 1.0064504  6.121579e-09  7.824319e-06
## ZNF229       25.89545     -1.5906382 1.6720902  2.654570e-05  2.004924e-02

DEA for Day25

DEAList_day25_HT <- readRDS(paste0(params$InputFolder, 'day25/Output/Savings/day25CbO.DEAList_HT.rds'))
DEAList_day25_AR <- readRDS(paste0(params$InputFolder, 'day25/Output/Savings/day25CbO.DEAList_AR.rds'))

DEAList_day25_HT
## $dds
## class: DESeqDataSet 
## dim: 17781 13 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17781): TSPAN6 TNMD ... PDCD6-AHRR LNCDAT
## rowData names(51): Gene EnsGene ... deviance maxCooks
## colnames(13): OLE_007 OLE_008 ... OLE_038 OLE_039
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 17781 rows and 6 columns
##                baseMean log2FoldChange     lfcSE      stat    pvalue      padj
##               <numeric>      <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6       1899.95350       0.126856 0.0916115  1.384712 0.1661405  0.416807
## TNMD            1.40474      -0.901158 1.7476042 -0.515653 0.6060966        NA
## DPM1          753.98864      -0.060679 0.0925993 -0.655286 0.5122838  0.757325
## SCYL3         324.26243      -0.123254 0.1218039 -1.011908 0.3115821  0.589861
## C1orf112      606.44497      -0.251886 0.0984460 -2.558627 0.0105086  0.061790
## ...                 ...            ...       ...       ...       ...       ...
## C8orf44       219.88820      0.0784975  0.163767  0.479325 0.6317071  0.834864
## C8orf44-SGK3    6.72668      1.5490628  1.385756  1.117847 0.2636323  0.539837
## NPBWR1          3.20140      0.6146274  1.355148  0.453550 0.6501526        NA
## PDCD6-AHRR     25.30042     -3.7720161  3.456649 -1.091235 0.2751695  0.552450
## LNCDAT          7.67620      1.7878652  0.828398  2.158219 0.0309108  0.138228
## 
## $HT$DEGs
##                baseMean log2FoldChange      lfcSE       stat        pvalue         padj
## CFH           26.094947      3.0438007 0.86098471   3.535255  4.073815e-04 4.584685e-03
## ENPP4        218.503431     -0.9487343 0.21605496  -4.391171  1.127417e-05 2.172581e-04
## SEMA3F       718.820104      0.7659644 0.21251021   3.604365  3.129171e-04 3.703258e-03
## HS3ST1       120.628365      3.0725465 0.47583325   6.457192  1.066638e-10 6.740345e-09
## HECW1        127.870718      0.8530832 0.28992535   2.942424  3.256542e-03 2.508466e-02
## KLHL13       292.946998     -0.7107625 0.25499351  -2.787375  5.313699e-03 3.680034e-02
## CYP26B1       64.560436      2.0414678 0.48878717   4.176599  2.959004e-05 4.910949e-04
## SKAP2         67.788433      1.0430165 0.35508420   2.937378  3.310006e-03 2.542631e-02
## COPZ2         30.807971     -1.3257562 0.43865978  -3.022288  2.508717e-03 2.029516e-02
## GCFC2        327.213096      0.6547935 0.19298996   3.392889  6.915961e-04 7.131446e-03
## CRLF1         45.918894      4.5005324 0.88501633   5.085254  3.671353e-07 1.065520e-05
## TMEM132A    3163.250522      0.8947162 0.11032366   8.109921  5.065256e-16 7.068565e-14
## CACNA1G      822.061921      1.5438853 0.18415734   8.383512  5.137135e-17 8.039856e-15
## TNFRSF12A    425.539393     -0.8334366 0.24696415  -3.374727  7.388895e-04 7.525263e-03
## DNAH9         80.569116      1.7959513 0.44432183   4.042006  5.299596e-05 8.075254e-04
## GAS7         262.330977      1.8874426 0.35909060   5.256174  1.470833e-07 4.673733e-06
## TKTL1         88.388265      1.0787253 0.23269003   4.635890  3.554051e-06 7.962278e-05
## MYLIP        349.607378      1.1112255 0.29307916   3.791554  1.497075e-04 1.978691e-03
## SYN1         200.742500     -0.7202241 0.16252394  -4.431495  9.358188e-06 1.839345e-04
## CDKL5        497.681947      0.6214245 0.15060416   4.126211  3.687892e-05 5.938216e-04
## CAMK1G        91.022896      0.7867750 0.23961322   3.283521  1.025190e-03 9.771104e-03
## CELSR3      3297.631944     -0.7586497 0.15822476  -4.794760  1.628700e-06 4.034646e-05
## NFIX          30.513303      3.0083096 0.54844426   5.485169  4.130737e-08 1.516959e-06
## ST3GAL1      263.451894      0.8552380 0.19714822   4.338046  1.437552e-05 2.674806e-04
## MAPK8IP2    1703.933691     -0.7127392 0.15402096  -4.627547  3.700227e-06 8.261867e-05
## TENM1        526.238303      0.7691039 0.23466349   3.277476  1.047398e-03 9.937521e-03
## PAX7        2966.607755      0.8615305 0.13395539   6.431473  1.263729e-10 7.867067e-09
## SEMA3G        43.262789      2.9643450 0.66247272   4.474667  7.653036e-06 1.542211e-04
## CD4           86.746953      1.8461830 0.40334497   4.577181  4.712834e-06 1.014410e-04
## TSPAN9       992.198040      0.6073611 0.17847193   3.403119  6.662132e-04 6.903717e-03
## PLAUR         90.804887      3.2057038 0.34596076   9.266091  1.930935e-20 3.849457e-18
## DCN          568.463747      3.0202352 0.81595333   3.701480  2.143453e-04 2.656801e-03
## CLDN11        99.291097     -1.2250425 0.42240986  -2.900128  3.730106e-03 2.788587e-02
## MAMLD1       261.098025      1.2937545 0.17315493   7.471659  7.919022e-14 8.611165e-12
## MTMR11       147.270254     -0.6954796 0.25397624  -2.738365  6.174555e-03 4.137280e-02
## CCDC88C     1154.376702      1.2318640 0.16530258   7.452176  9.181304e-14 9.855776e-12
## BID          202.367418      0.9238731 0.22559114   4.095343  4.215433e-05 6.653313e-04
## WWTR1       1608.891689      1.2790136 0.19934825   6.415976  1.399234e-10 8.614549e-09
## ATP1A2      5466.677387      0.7011471 0.15398879   4.553235  5.282723e-06 1.117820e-04
## ZNF582       106.237060     -1.1563022 0.19672741  -5.877687  4.160376e-09 1.914002e-07
## PHLDB1      2326.554528      0.6739143 0.07190713   9.372008  7.116535e-21 1.453335e-18
## MARCO         20.098400     -2.4041912 0.84248337  -2.853696  4.321389e-03 3.139522e-02
## SNAI2        223.847963      1.6537623 0.42478656   3.893160  9.894665e-05 1.389391e-03
## CD74         101.752401      0.7251838 0.23339605   3.107095  1.889354e-03 1.612595e-02
## HGF           48.216629      7.3818414 1.62787017   4.534662  5.769574e-06 1.204704e-04
## ADGRA2       324.830161      3.5851638 0.56570418   6.337524  2.334869e-10 1.381615e-08
## RUNX3          6.872916      4.3332663 1.30237202   3.327211  8.771998e-04 8.646020e-03
## SERPINB1      51.905708     -0.8330960 0.30999969  -2.687409  7.200871e-03 4.658346e-02
## ABCC2         77.290170      1.9656992 0.48374511   4.063502  4.834192e-05 7.468024e-04
## FAS          150.275268     -1.1455279 0.26385194  -4.341556  1.414775e-05 2.641229e-04
## ARNTL2       174.888558     -0.9497172 0.27372988  -3.469542  5.213472e-04 5.643491e-03
## LRRC7        108.046025     -0.9442942 0.32537589  -2.902164  3.705946e-03 2.774556e-02
## APBA2       1686.739077      1.0059252 0.10281602   9.783739  1.322331e-22 3.209241e-20
## TMSB10      7552.547506      0.7227666 0.17218558   4.197603  2.697556e-05 4.562956e-04
## TLL1          12.651016     -1.9666972 0.71940567  -2.733781  6.261176e-03 4.177277e-02
## VCAN       15304.419355      1.0372404 0.20075009   5.166824  2.381054e-07 7.236501e-06
## RAI14       3657.542133      0.6989235 0.12558277   5.565441  2.614904e-08 1.013638e-06
## CDH10        433.931740     -0.9047519 0.15316677  -5.906972  3.484523e-09 1.620884e-07
## RIPOR3        16.756729      1.6037723 0.50664697   3.165463  1.548363e-03 1.371899e-02
## USH2A         57.012639     -1.3564541 0.48573894  -2.792558  5.229311e-03 3.630599e-02
## ARAP2        124.762877     -1.4244012 0.20776433  -6.855851  7.088939e-12 5.445476e-10
## LMO3        1129.207946      0.9787634 0.20766816   4.713113  2.439614e-06 5.786654e-05
## COL9A2       216.418926      0.7856526 0.24231844   3.242232  1.185975e-03 1.098470e-02
## ELN          343.750002      1.0419168 0.32486352   3.207245  1.340130e-03 1.215700e-02
## PPP1R3F      287.110950     -0.6087422 0.13676400  -4.451041  8.545510e-06 1.701583e-04
## COL23A1      299.891592      1.5286147 0.37891028   4.034239  5.477951e-05 8.309219e-04
## HOMER3       973.537438      0.6669470 0.08321356   8.014884  1.102414e-15 1.500896e-13
## ALX4          62.424694      3.7275951 0.58540511   6.367548  1.920741e-10 1.161182e-08
## LAMA3         51.721896     -1.3309408 0.47013709  -2.830963  4.640806e-03 3.328263e-02
## PHPT1       2017.187145     -0.6956466 0.09390555  -7.407939  1.282773e-13 1.309837e-11
## FOXC1        169.732191      0.9697764 0.31302112   3.098118  1.947537e-03 1.647144e-02
## PLEKHH1      456.598620      1.2480265 0.17167006   7.269913  3.597184e-13 3.442197e-11
## PARP12        65.279914     -0.9124330 0.29888380  -3.052802  2.267156e-03 1.868395e-02
## SLC2A3      1089.408979     -1.1424268 0.18184910  -6.282279  3.336449e-10 1.933293e-08
## PSD          918.925574     -0.7364148 0.15685285  -4.694940  2.666846e-06 6.205291e-05
## RIMBP2       339.775566      0.9608767 0.19299132   4.978860  6.396000e-07 1.755859e-05
## COL11A1     2620.885828     -0.8055683 0.13098350  -6.150151  7.740928e-10 4.102202e-08
## PRDM6         46.147992     -1.3272232 0.42458154  -3.125956  1.772281e-03 1.532195e-02
## GUCY1B1      359.307001      0.8520241 0.21507372   3.961545  7.446645e-05 1.084361e-03
## CDH3         115.083764      1.4311358 0.31809854   4.499033  6.826333e-06 1.404346e-04
## TM7SF3      1749.910744     -0.7496604 0.11327127  -6.618275  3.634148e-11 2.453929e-09
## NGFR        2329.716326      2.0779836 0.44023738   4.720143  2.356784e-06 5.606067e-05
## SNCAIP       260.170680      1.0266463 0.23739737   4.324590  1.528158e-05 2.815240e-04
## SLC9A3R2      65.870811      1.7960836 0.40511657   4.433498  9.271629e-06 1.826620e-04
## NTN1         121.905642      2.4032932 0.47150978   5.097017  3.450482e-07 1.004900e-05
## ERBB3        843.390203      4.6459828 0.64193307   7.237488  4.570716e-13 4.300068e-11
## ROPN1         12.544528      4.5740872 1.07475956   4.255917  2.081942e-05 3.646883e-04
## ANKRD44      306.039989      1.0254039 0.23424500   4.377485  1.200568e-05 2.295058e-04
## PRKCQ         41.457806      1.4665457 0.44802494   3.273357  1.062781e-03 1.007206e-02
## ME1           35.287912     -1.5880512 0.42333570  -3.751281  1.759333e-04 2.261074e-03
## CTNNA2      1875.110826     -0.8819497 0.18519362  -4.762312  1.913878e-06 4.658401e-05
## TIE1          95.688520      1.6811874 0.32979041   5.097745  3.437233e-07 1.002786e-05
## STAG3         76.435177      0.8939669 0.23021358   3.883206  1.030879e-04 1.436199e-03
## CBFB        1437.870064      0.6161926 0.11046607   5.578116  2.431371e-08 9.468775e-07
## LAPTM4A     1508.957366      0.8798920 0.22658032   3.883356  1.030246e-04 1.436199e-03
## TGFBR3       569.826299      0.6821606 0.21720243   3.140667  1.685634e-03 1.467132e-02
## FGF10         84.326946     -2.0245121 0.58208943  -3.478009  5.051536e-04 5.507359e-03
## ST6GALNAC2     5.409746      4.4177512 1.61194721   2.740630  6.132148e-03 4.117440e-02
## NCK2        1313.614599      0.6241392 0.08596429   7.260447  3.858123e-13 3.670916e-11
## LMCD1        140.988752     -0.8247264 0.16424137  -5.021429  5.128839e-07 1.441066e-05
## CDH19        185.249695      8.3458917 1.67515216   4.982169  6.287537e-07 1.731761e-05
## SLC6A15      587.038713     -0.6429582 0.21235197  -3.027795  2.463452e-03 1.999659e-02
## SPEG         600.513852      0.8828196 0.18699373   4.721119  2.345510e-06 5.587185e-05
## TRNT1        399.036066     -0.5891796 0.16030693  -3.675322  2.375492e-04 2.901531e-03
## STK10        305.451866      0.6122181 0.17315251   3.535716  4.066716e-04 4.579773e-03
## PANX2         85.288132     -1.1836661 0.27361299  -4.326060  1.518002e-05 2.799611e-04
## PTGS2         23.363877      4.4367382 0.88638888   5.005408  5.574376e-07 1.553220e-05
## MAP3K13      350.872641     -1.6218423 0.24247519  -6.688694  2.251716e-11 1.577709e-09
## ST6GAL1      946.031424      1.1716192 0.11050602  10.602312  2.907041e-26 8.540580e-24
## SEMA3C       917.956652      1.3113320 0.30492548   4.300500  1.704133e-05 3.095164e-04
## ZNF37A       212.146852      6.1642995 0.35274076  17.475438  2.204447e-68 4.101741e-65
## FSCN1       7818.193996      0.8229400 0.11900671   6.915072  4.676249e-12 3.642254e-10
## PAX2         295.741304      3.4855765 0.76673335   4.546009  5.467279e-06 1.147983e-04
## SLC46A1      163.629920     -0.8014018 0.22901770  -3.499301  4.664801e-04 5.156221e-03
## PAG1         795.875188      1.3442681 0.24552328   5.475115  4.372288e-08 1.584812e-06
## MCAM         275.226668      2.6124017 0.43289897   6.034668  1.592895e-09 7.845474e-08
## CTTNBP2      349.544411      1.1712458 0.24425943   4.795089  1.626023e-06 4.033982e-05
## CAPN6         39.711229      3.6216186 1.01180642   3.579359  3.444378e-04 4.005525e-03
## ITGA8        150.240069      1.9935254 0.43789049   4.552566  5.299552e-06 1.117820e-04
## SYNJ2        148.855847     -0.8343846 0.23869065  -3.495674  4.728664e-04 5.223364e-03
## ADCY2        691.221145     -0.6513854 0.18203195  -3.578412  3.456878e-04 4.017271e-03
## BRINP1       125.706735      1.6155204 0.25002670   6.461391  1.037445e-10 6.580705e-09
## RUNX1T1      290.240488      1.2433708 0.33783301   3.680430  2.328408e-04 2.850257e-03
## FKBP7        460.597114      0.8688453 0.15958166   5.444519  5.194566e-08 1.862702e-06
## TNS1         652.603607      1.4915821 0.27164102   5.491005  3.996538e-08 1.474141e-06
## MOXD1        932.633094      2.7412323 0.76214017   3.596756  3.222104e-04 3.794469e-03
## DCT           59.062425      0.8596046 0.27927388   3.077999  2.083959e-03 1.742285e-02
## SESN1        941.182511     -1.2002453 0.17017468  -7.053019  1.750767e-12 1.503505e-10
## COL5A3       102.867590      3.3585265 0.54074259   6.210952  5.266440e-10 2.920258e-08
## MEF2C        239.182267      1.2817884 0.37327671   3.433882  5.950021e-04 6.310263e-03
## AACS         560.420968      0.6859040 0.12957774   5.293378  1.200773e-07 3.945769e-06
## PCDHA6       249.677359      4.6732955 0.21853234  21.384915 1.846248e-101 1.030576e-97
## SERTAD4      389.392252      1.3098770 0.25199420   5.198045  2.013959e-07 6.233967e-06
## OPRK1         48.580938     -1.4590153 0.46120667  -3.163474  1.558983e-03 1.378391e-02
## LYRM2       1131.131783     -1.0249882 0.08361564 -12.258331  1.515895e-34 7.051436e-32
## SLC27A5       85.311999     -0.7216511 0.21425030  -3.368262  7.564374e-04 7.669595e-03
## FAM234B      495.856221     -0.6176869 0.10503019  -5.881042  4.076929e-09 1.891198e-07
## SLCO1A2      100.222222      2.9006897 0.39031546   7.431655  1.072475e-13 1.136688e-11
## NKAIN1      1420.368524      1.0787586 0.16219745   6.650897  2.913113e-11 1.999303e-09
## COL16A1      100.782242      1.9727019 0.62628293   3.149857  1.633502e-03 1.429933e-02
## EFR3B       1670.269246      0.5882143 0.12852987   4.576480  4.728652e-06 1.016509e-04
## PREP         897.889194      0.5984011 0.14781693   4.048258  5.160016e-05 7.892399e-04
## ABCB1         86.830515     -1.8460473 0.57134914  -3.231032  1.233442e-03 1.133034e-02
## WNT11         29.349678      2.2819322 0.52777193   4.323709  1.534277e-05 2.823406e-04
## PPEF1         37.653044      1.8522545 0.51834470   3.573403  3.523719e-04 4.080788e-03
## BAX         1038.927079     -0.9168254 0.13620937  -6.731001  1.684999e-11 1.232183e-09
## ADAMTS2      214.063991      1.3983249 0.18052160   7.746025  9.481367e-15 1.142266e-12
## MMP2        2109.069578      1.1129752 0.16063063   6.928786  4.244686e-12 3.352901e-10
## GNAO1       1183.611230     -0.9323370 0.27333493  -3.410969  6.473247e-04 6.753956e-03
## SH3BP2      1203.121984      0.7137084 0.12368230   5.770497  7.903810e-09 3.428943e-07
## NID2         202.360977      2.3530468 0.44102439   5.335412  9.532791e-08 3.238055e-06
## PHACTR3      115.215407      1.1253445 0.37658951   2.988252  2.805776e-03 2.231032e-02
## TFAP2C        78.284764      4.2074733 1.00203121   4.198944  2.681622e-05 4.545186e-04
## DOCK9        194.313627      0.6715095 0.21653363   3.101179  1.927520e-03 1.632695e-02
## C3orf18      145.755327     -0.6280050 0.20965484  -2.995424  2.740640e-03 2.190681e-02
## ARHGAP28     720.983385      1.1497726 0.26298196   4.372059  1.230803e-05 2.342162e-04
## SMOX         291.626581      0.8708279 0.22848598   3.811297  1.382395e-04 1.853450e-03
## SLC4A11       42.453434     -0.8773281 0.30216221  -2.903500  3.690166e-03 2.767213e-02
## FXYD5         51.429416      1.5641153 0.48792156   3.205670  1.347486e-03 1.220390e-02
## PITPNM2      283.322341     -0.7924381 0.12546570  -6.315973  2.684662e-10 1.571935e-08
## LAMB1       1886.846162      2.4071061 0.46865253   5.136228  2.803081e-07 8.352384e-06
## CCDC80      1509.048047     -1.6637058 0.24371984  -6.826304  8.713002e-12 6.662463e-10
## WDR76        478.334624     -0.8356596 0.22367225  -3.736090  1.869038e-04 2.378337e-03
## CAPN3         44.501543      0.8687641 0.31421288   2.764890  5.694195e-03 3.885697e-02
## TBX15         72.509651      2.7047557 0.56373371   4.797931  1.603126e-06 3.988998e-05
## COL9A3       242.331908      2.3793395 0.35512495   6.700007  2.084103e-11 1.480981e-09
##  [ reached 'max' / getOption("max.print") -- omitted 1345 rows ]
## 
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 17781 rows and 5 columns
##                baseMean log2FoldChange     lfcSE    pvalue      padj
##               <numeric>      <numeric> <numeric> <numeric> <numeric>
## TSPAN6       1899.95350      0.0661316 0.0759612 0.1661405  0.416807
## TNMD            1.40474     -0.0348380 0.3563090 0.6060966        NA
## DPM1          753.98864     -0.0273858 0.0649198 0.5122838  0.757325
## SCYL3         324.26243     -0.0504830 0.0852623 0.3115821  0.589861
## C1orf112      606.44497     -0.1677184 0.1002672 0.0105086  0.061790
## ...                 ...            ...       ...       ...       ...
## C8orf44       219.88820      0.0241253  0.092974 0.6317071  0.834864
## C8orf44-SGK3    6.72668      0.0894832  0.394144 0.2636323  0.539837
## NPBWR1          3.20140      0.0309958  0.313306 0.6501526        NA
## PDCD6-AHRR     25.30042     -0.0752447  0.566431 0.2751695  0.552450
## LNCDAT          7.67620      0.3241569  0.589033 0.0309108  0.138228
## 
## $HT$DEGsAshr
##                baseMean log2FoldChange      lfcSE        pvalue         padj
## CFH           26.094947      1.8204589 1.20690149  4.073815e-04 4.584685e-03
## ENPP4        218.503431     -0.8351669 0.23132770  1.127417e-05 2.172581e-04
## SEMA3F       718.820104      0.6111376 0.25208213  3.129171e-04 3.703258e-03
## HS3ST1       120.628365      2.8755673 0.49877068  1.066638e-10 6.740345e-09
## CYP26B1       64.560436      1.6690993 0.56624201  2.959004e-05 4.910949e-04
## SKAP2         67.788433      0.5908787 0.43681468  3.310006e-03 2.542631e-02
## COPZ2         30.807971     -0.7332842 0.55007598  2.508717e-03 2.029516e-02
## CRLF1         45.918894      4.0226092 0.96985366  3.671353e-07 1.065520e-05
## TMEM132A    3163.250522      0.8672252 0.11105665  5.065256e-16 7.068565e-14
## CACNA1G      822.061921      1.4933118 0.18716908  5.137135e-17 8.039856e-15
## TNFRSF12A    425.539393     -0.6173661 0.30199339  7.388895e-04 7.525263e-03
## DNAH9         80.569116      1.4485745 0.52139554  5.299596e-05 8.075254e-04
## GAS7         262.330977      1.7067523 0.37643787  1.470833e-07 4.673733e-06
## TKTL1         88.388265      0.9598199 0.24567400  3.554051e-06 7.962278e-05
## MYLIP        349.607378      0.8910395 0.34283487  1.497075e-04 1.978691e-03
## SYN1         200.742500     -0.6452231 0.17476732  9.358188e-06 1.839345e-04
## CELSR3      3297.631944     -0.6933477 0.16543633  1.628700e-06 4.034646e-05
## NFIX          30.513303      2.7266283 0.58613440  4.130737e-08 1.516959e-06
## ST3GAL1      263.451894      0.7542074 0.21215554  1.437552e-05 2.674806e-04
## MAPK8IP2    1703.933691     -0.6470743 0.16330372  3.700227e-06 8.261867e-05
## PAX7        2966.607755      0.8200388 0.13540494  1.263729e-10 7.867067e-09
## SEMA3G        43.262789      2.4864249 0.76617647  7.653036e-06 1.542211e-04
## CD4           86.746953      1.5982950 0.43935052  4.712834e-06 1.014410e-04
## PLAUR         90.804887      3.1141296 0.35404172  1.930935e-20 3.849457e-18
## DCN          568.463747      2.0128626 1.12462857  2.143453e-04 2.656801e-03
## CLDN11        99.291097     -0.6366996 0.51610088  3.730106e-03 2.788587e-02
## MAMLD1       261.098025      1.2403644 0.17667022  7.919022e-14 8.611165e-12
## CCDC88C     1154.376702      1.1810600 0.16842548  9.181304e-14 9.855776e-12
## BID          202.367418      0.7907721 0.24950829  4.215433e-05 6.653313e-04
## WWTR1       1608.891689      1.2063943 0.20466736  1.399234e-10 8.614549e-09
## ATP1A2      5466.677387      0.6339970 0.16433042  5.282723e-06 1.117820e-04
## ZNF582       106.237060     -1.0791550 0.20192369  4.160376e-09 1.914002e-07
## PHLDB1      2326.554528      0.6611069 0.07213194  7.116535e-21 1.453335e-18
## MARCO         20.098400     -0.8193686 0.95328420  4.321389e-03 3.139522e-02
## SNAI2        223.847963      1.3021122 0.50868468  9.894665e-05 1.389391e-03
## HGF           48.216629      6.0858591 1.96992360  5.769574e-06 1.204704e-04
## ADGRA2       324.830161      3.3569809 0.59455300  2.334869e-10 1.381615e-08
## RUNX3          6.872916      1.8359420 1.82162316  8.771998e-04 8.646020e-03
## ABCC2         77.290170      1.5786640 0.57048606  4.834192e-05 7.468024e-04
## FAS          150.275268     -0.9925455 0.28619963  1.414775e-05 2.641229e-04
## ARNTL2       174.888558     -0.7129411 0.33315937  5.213472e-04 5.643491e-03
## APBA2       1686.739077      0.9834384 0.10348487  1.322331e-22 3.209241e-20
## TMSB10      7552.547506      0.6345593 0.18932762  2.697556e-05 4.562956e-04
## TLL1          12.651016     -0.6706594 0.78335163  6.261176e-03 4.177277e-02
## VCAN       15304.419355      0.9497228 0.20710314  2.381054e-07 7.236501e-06
## RAI14       3657.542133      0.6583681 0.12842594  2.614904e-08 1.013638e-06
## CDH10        433.931740     -0.8512471 0.15552753  3.484523e-09 1.620884e-07
## RIPOR3        16.756729      0.9179563 0.65243692  1.548363e-03 1.371899e-02
## USH2A         57.012639     -0.6146691 0.57150844  5.229311e-03 3.630599e-02
## ARAP2        124.762877     -1.3532752 0.21314720  7.088939e-12 5.445476e-10
## LMO3        1129.207946      0.8794423 0.21743646  2.439614e-06 5.786654e-05
## ELN          343.750002      0.6919265 0.40693564  1.340130e-03 1.215700e-02
## COL23A1      299.891592      1.2484701 0.43864340  5.477951e-05 8.309219e-04
## HOMER3       973.537438      0.6496463 0.08363206  1.102414e-15 1.500896e-13
## ALX4          62.424694      3.4955547 0.61405445  1.920741e-10 1.161182e-08
## LAMA3         51.721896     -0.6299780 0.56155278  4.640806e-03 3.328263e-02
## PHPT1       2017.187145     -0.6738356 0.09449508  1.282773e-13 1.309837e-11
## FOXC1        169.732191      0.6189686 0.39024906  1.947537e-03 1.647144e-02
## PLEKHH1      456.598620      1.1937296 0.17514620  3.597184e-13 3.442197e-11
## SLC2A3      1089.408979     -1.0763779 0.18590339  3.336449e-10 1.933293e-08
## PSD          918.925574     -0.6703328 0.16521941  2.666846e-06 6.205291e-05
## RIMBP2       339.775566      0.8758933 0.19963762  6.396000e-07 1.755859e-05
## COL11A1     2620.885828     -0.7647290 0.13254546  7.740928e-10 4.102202e-08
## PRDM6         46.147992     -0.7883202 0.53931473  1.772281e-03 1.532195e-02
## GUCY1B1      359.307001      0.7206140 0.24218923  7.446645e-05 1.084361e-03
## CDH3         115.083764      1.2443502 0.34532395  6.826333e-06 1.404346e-04
## TM7SF3      1749.910744     -0.7185034 0.11429207  3.634148e-11 2.453929e-09
## NGFR        2329.716326      1.8108795 0.47550455  2.356784e-06 5.606067e-05
## SNCAIP       260.170680      0.8940764 0.25639396  1.528158e-05 2.815240e-04
## SLC9A3R2      65.870811      1.5349417 0.44752509  9.271629e-06 1.826620e-04
## NTN1         121.905642      2.1378001 0.50141293  3.450482e-07 1.004900e-05
## ERBB3        843.390203      4.4347840 0.65837102  4.570716e-13 4.300068e-11
## ROPN1         12.544528      3.6582079 1.38966794  2.081942e-05 3.646883e-04
## ANKRD44      306.039989      0.8973202 0.25167882  1.200568e-05 2.295058e-04
## PRKCQ         41.457806      0.9258806 0.57631846  1.062781e-03 1.007206e-02
## ME1           35.287912     -1.2100403 0.51861987  1.759333e-04 2.261074e-03
## CTNNA2      1875.110826     -0.7989689 0.19316099  1.913878e-06 4.658401e-05
## TIE1          95.688520      1.5137529 0.34776511  3.437233e-07 1.002786e-05
## STAG3         76.435177      0.7442613 0.26232508  1.030879e-04 1.436199e-03
## LAPTM4A     1508.957366      0.7335021 0.25812226  1.030246e-04 1.436199e-03
## FGF10         84.326946     -1.3137151 0.76715974  5.051536e-04 5.507359e-03
## ST6GALNAC2     5.409746      0.7703031 1.42114751  6.132148e-03 4.117440e-02
## NCK2        1313.614599      0.6050463 0.08671326  3.858123e-13 3.670916e-11
## LMCD1        140.988752     -0.7586322 0.16953054  5.128839e-07 1.441066e-05
## CDH19        185.249695      7.1952215 1.78966970  6.287537e-07 1.731761e-05
## SPEG         600.513852      0.7979340 0.19546694  2.345510e-06 5.587185e-05
## PANX2         85.288132     -1.0220999 0.29793286  1.518002e-05 2.799611e-04
## PTGS2         23.363877      3.9432427 0.97911467  5.574376e-07 1.553220e-05
## MAP3K13      350.872641     -1.5349610 0.24883485  2.251716e-11 1.577709e-09
## ST6GAL1      946.031424      1.1483420 0.11147459  2.907041e-26 8.540580e-24
## SEMA3C       917.956652      1.1228890 0.33554589  1.704133e-05 3.095164e-04
## ZNF37A       212.146852      6.1169572 0.35362701  2.204447e-68 4.101741e-65
## FSCN1       7818.193996      0.7897505 0.11997776  4.676249e-12 3.642254e-10
## PAX2         295.741304      2.9507472 0.89484931  5.467279e-06 1.147983e-04
## SLC46A1      163.629920     -0.6198474 0.27568570  4.664801e-04 5.156221e-03
## PAG1         795.875188      1.2358462 0.25531771  4.372288e-08 1.584812e-06
## MCAM         275.226668      2.4134143 0.45148804  1.592895e-09 7.845474e-08
## CTTNBP2      349.544411      1.0484293 0.25692016  1.626023e-06 4.033982e-05
## CAPN6         39.711229      2.1303538 1.46250565  3.444378e-04 4.005525e-03
## ITGA8        150.240069      1.7149465 0.47957243  5.299552e-06 1.117820e-04
## SYNJ2        148.855847     -0.6418755 0.28779687  4.728664e-04 5.223364e-03
## BRINP1       125.706735      1.5222507 0.25718006  1.037445e-10 6.580705e-09
## RUNX1T1      290.240488      0.9581089 0.40736905  2.328408e-04 2.850257e-03
## FKBP7        460.597114      0.8091182 0.16289516  5.194566e-08 1.862702e-06
## TNS1         652.603607      1.3697167 0.28326789  3.996538e-08 1.474141e-06
## MOXD1        932.633094      1.7574235 1.04337171  3.222104e-04 3.794469e-03
## SESN1        941.182511     -1.1450055 0.17356136  1.750767e-12 1.503505e-10
## COL5A3       102.867590      3.1297734 0.57024997  5.266440e-10 2.920258e-08
## MEF2C        239.182267      0.9037346 0.46872195  5.950021e-04 6.310263e-03
## AACS         560.420968      0.6415484 0.13357424  1.200773e-07 3.945769e-06
## PCDHA6       249.677359      4.6503431 0.21899197 1.846248e-101 1.030576e-97
## SERTAD4      389.392252      1.1919451 0.26321914  2.013959e-07 6.233967e-06
## OPRK1         48.580938     -0.8615249 0.59078709  1.558983e-03 1.378391e-02
## LYRM2       1131.131783     -1.0103273 0.08398768  1.515895e-34 7.051436e-32
## FAM234B      495.856221     -0.5877389 0.10752818  4.076929e-09 1.891198e-07
## SLCO1A2      100.222222      2.7616542 0.40367926  1.072475e-13 1.136688e-11
## NKAIN1      1420.368524      1.0243981 0.16498503  2.913113e-11 1.999303e-09
## COL16A1      100.782242      1.0261519 0.81043549  1.633502e-03 1.429933e-02
## ABCB1         86.830515     -1.0520829 0.74611367  1.233442e-03 1.133034e-02
## WNT11         29.349678      1.8942069 0.60286471  1.534277e-05 2.823406e-04
## PPEF1         37.653044      1.2883648 0.66781463  3.523719e-04 4.080788e-03
## BAX         1038.927079     -0.8751035 0.13768150  1.684999e-11 1.232183e-09
## ADAMTS2      214.063991      1.3445415 0.18416067  9.481367e-15 1.142266e-12
## MMP2        2109.069578      1.0608657 0.16339637  4.244686e-12 3.352901e-10
## GNAO1       1183.611230     -0.6881921 0.33474421  6.473247e-04 6.753956e-03
## SH3BP2      1203.121984      0.6751120 0.12590180  7.903810e-09 3.428943e-07
## NID2         202.360977      2.1206132 0.46378080  9.532791e-08 3.238055e-06
## PHACTR3      115.215407      0.6435296 0.46771759  2.805776e-03 2.231032e-02
## TFAP2C        78.284764      3.3232530 1.30405015  2.681622e-05 4.545186e-04
## ARHGAP28     720.983385      0.9988736 0.28446912  1.230803e-05 2.342162e-04
## SMOX         291.626581      0.7175695 0.26314324  1.382395e-04 1.853450e-03
## FXYD5         51.429416      0.9283993 0.62954563  1.347486e-03 1.220390e-02
## PITPNM2      283.322341     -0.7548270 0.12680947  2.684662e-10 1.571935e-08
## LAMB1       1886.846162      2.1459243 0.49751556  2.803081e-07 8.352384e-06
## CCDC80      1509.048047     -1.5780054 0.24964565  8.713002e-12 6.662463e-10
## WDR76        478.334624     -0.6811357 0.26046380  1.869038e-04 2.378337e-03
## TBX15         72.509651      2.3508271 0.61864600  1.603126e-06 3.988998e-05
## COL9A3       242.331908      2.2361190 0.36464302  2.084103e-11 1.480981e-09
## COMT         452.481912     -5.9653802 0.37944297  4.504574e-57 6.857599e-54
## MAP3K1      1148.013026      0.6874149 0.18612274  9.461281e-06 1.855253e-04
## PTGS1         31.509437      1.1099582 0.48366641  2.144986e-04 2.656801e-03
## CYP26A1       98.213130     -0.8634663 0.78255964  2.843182e-03 2.254352e-02
## SORBS1       909.124977      1.6123366 0.21944433  7.402449e-15 9.114809e-13
## MYO3A        557.286642     -0.5931849 0.13312794  5.000475e-07 1.412107e-05
## ITPR3        189.684498      1.3142699 0.41928637  2.504339e-05 4.274990e-04
## DSP          380.546181      0.7302231 0.65140214  3.668967e-03 2.753946e-02
## PCSK5        244.525493      0.6110098 0.29325472  6.836661e-04 7.071253e-03
## MADCAM1       54.581374      1.1979226 0.31208287  3.240233e-06 7.370437e-05
## P2RX6        137.787116      0.5925481 0.26607335  5.057900e-04 5.508873e-03
## MFNG         267.898872      0.7451119 0.40427475  9.140961e-04 8.946495e-03
## LGALS1       193.581100      2.0250769 0.56389737  4.013803e-06 8.774823e-05
## SOX10        483.139150      6.3790203 1.41654487  1.289535e-07 4.168831e-06
## TIMP3        871.015109      1.8614504 0.54559831  7.704417e-06 1.550699e-04
## IL2RB         13.660909      2.1325269 1.25430852  2.280388e-04 2.795561e-03
## MLC1          44.178387     -0.8112794 0.48961928  1.173473e-03 1.089905e-02
## RIN3         141.716968      0.6028604 0.31142311  9.582589e-04 9.269053e-03
## SIX4         251.213438      0.7907314 0.22251487  1.404329e-05 2.630526e-04
## DHRS2         54.781227      1.2420834 0.33526578  4.903932e-06 1.048142e-04
## NFATC2        79.980931      2.9494065 0.48055909  1.090948e-11 8.266520e-10
## BMP7        1638.740410      0.9727772 0.17291140  1.110669e-09 5.636143e-08
## CTSZ         190.448842     -1.2491211 0.35751619  9.584436e-06 1.877204e-04
## SLCO4A1       37.472438      0.8858873 0.44832350  5.564887e-04 5.962226e-03
## COL20A1       31.422993      3.3312918 0.61835071  9.796481e-10 5.063329e-08
## CHRNA4       296.314528      0.7991794 0.28413775  1.029810e-04 1.436199e-03
## ISM1          63.701681      1.0153693 0.63243987  9.245800e-04 9.012233e-03
## PDYN          26.279039      0.7820848 0.56489018  2.069371e-03 1.733551e-02
## PLCB4        705.393857      0.9261918 0.24646436  6.231323e-06 1.291457e-04
## MYL9          37.302147     -1.5761753 0.49775004  1.857695e-05 3.323607e-04
## MROH8         78.954114     -0.6126304 0.25303087  3.148616e-04 3.720055e-03
## SNTA1        166.797244     -0.5888797 0.17224662  2.130902e-05 3.717093e-04
## SYP          836.231919     -0.9039093 0.17559993  1.755877e-08 7.051298e-07
## ASB9           6.741230      1.5457888 1.74469868  1.365990e-03 1.233255e-02
## PCYT1B       160.992279      0.6371812 0.37885514  1.543869e-03 1.368641e-02
## TIMP1        445.231612     -0.8863550 0.35883069  2.001202e-04 2.514038e-03
## KLHL4        262.136971     -0.7557330 0.27356375  1.220067e-04 1.657034e-03
## SYTL4         20.803237     -0.8662000 0.65733687  1.987567e-03 1.675921e-02
## RUBCNL        82.459803      1.6509604 0.32246393  9.038271e-09 3.880895e-07
## ACP5           6.852640      1.0745801 1.29709462  2.725655e-03 2.179743e-02
## FGF9         328.553077      0.6466550 0.24839585  1.980994e-04 2.494265e-03
## FLT1          58.806278     -1.1250030 0.39891352  6.668891e-05 9.848082e-04
## MAPK3        948.417335     -1.0533247 0.09279005  3.892485e-31 1.481444e-28
## GDPD3         45.518635     -1.2023284 0.30377389  2.089265e-06 5.012440e-05
## CRISPLD2      73.086545      1.7311632 0.42183952  8.564777e-07 2.258469e-05
## CRYM          68.163353      0.8993002 0.63481968  1.572293e-03 1.387961e-02
## SLC6A2        10.232749      1.5828511 1.18970999  6.886514e-04 7.105457e-03
## AP3B2       1357.167977     -0.7848479 0.12349956  2.091538e-11 1.480981e-09
## CTSH          74.155863     -1.1046362 0.23612722  1.158029e-07 3.824923e-06
## BMF         1449.952680      0.9945312 0.13813956  3.679141e-14 4.249027e-12
## TRPA1         11.226665      0.9709660 0.85960104  2.224268e-03 1.841206e-02
## CPQ           27.090485     -0.5914849 0.47881376  4.147806e-03 3.037130e-02
## CALB1        737.727904     -2.3041071 0.24338084  7.334321e-23 1.806184e-20
## SFRP1       1447.047551      0.6865710 0.25593851  1.582987e-04 2.068083e-03
## NIPAL2        32.799299     -0.6766169 0.52283634  3.043752e-03 2.383387e-02
## PLAT         345.386781      1.1213317 0.36062456  3.267704e-05 5.333428e-04
## GSDMD         34.351513     -2.9197826 0.39464009  1.775085e-15 2.378046e-13
## OLFM2        334.559507      0.9191335 0.23977827  4.882146e-06 1.046817e-04
## SLC1A6       183.532876      0.9616731 0.26051185  7.364988e-06 1.494959e-04
## KCNN1        195.412604      0.8760081 0.29538848  6.450009e-05 9.567037e-04
## TFPI2        192.192277     -2.3096581 0.38878050  6.071385e-11 3.987114e-09
## DLX5           6.841212      1.3995296 1.64847563  1.686596e-03 1.467207e-02
##  [ reached 'max' / getOption("max.print") -- omitted 1037 rows ]
DEAList_day25_AR
## $dds
## class: DESeqDataSet 
## dim: 17781 13 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17781): TSPAN6 TNMD ... PDCD6-AHRR LNCDAT
## rowData names(51): Gene EnsGene ... deviance maxCooks
## colnames(13): OLE_007 OLE_008 ... OLE_038 OLE_039
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 17781 rows and 6 columns
##                baseMean log2FoldChange     lfcSE       stat     pvalue      padj
##               <numeric>      <numeric> <numeric>  <numeric>  <numeric> <numeric>
## TSPAN6       1899.95350    -0.00321804  0.107759 -0.0298632 0.97617617 0.9969430
## TNMD            1.40474    -2.67322743  2.191542 -1.2197928 0.22254342        NA
## DPM1          753.98864    -0.12588099  0.109614 -1.1484013 0.25080293 0.7661892
## SCYL3         324.26243    -0.10145290  0.143237 -0.7082863 0.47876749 0.8878547
## C1orf112      606.44497    -0.37363020  0.115953 -3.2222548 0.00127186 0.0876281
## ...                 ...            ...       ...        ...        ...       ...
## C8orf44       219.88820       0.164147  0.192447   0.852950   0.393687  0.848049
## C8orf44-SGK3    6.72668       0.282797  1.577018   0.179324   0.857683  0.981561
## NPBWR1          3.20140       0.428658  1.613866   0.265609   0.790540        NA
## PDCD6-AHRR     25.30042      -2.044981  4.131004  -0.495033   0.620577  0.938008
## LNCDAT          7.67620      -0.939696  1.016744  -0.924221   0.355371  0.825025
## 
## $AR$DEGs
##                   baseMean log2FoldChange     lfcSE       stat       pvalue         padj
## ZMYND10           57.19480      1.3624567 0.3892638   3.500086 4.651089e-04 4.624891e-02
## CACNA1G          822.06192      0.7856551 0.2171074   3.618739 2.960425e-04 3.493302e-02
## NRXN3            125.92310      1.5316628 0.3828391   4.000800 6.312865e-05 1.247513e-02
## DSG2             537.93484      1.3351256 0.3360632   3.972840 7.102070e-05 1.354513e-02
## UBE2T            701.97049     -1.0105319 0.1132986  -8.919190 4.697111e-19 1.284034e-15
## OSBPL6           248.89844     -0.6141677 0.1721876  -3.566851 3.612962e-04 4.027025e-02
## ZNF506           590.46712     -1.0754446 0.1436865  -7.484663 7.173113e-14 1.593125e-10
## ZNF671           204.82774     -1.0215515 0.2865220  -3.565351 3.633701e-04 4.027025e-02
## HSD17B14         169.46894      1.0153134 0.2645589   3.837760 1.241619e-04 2.036503e-02
## BMP7            1638.74041      0.9745700 0.2000345   4.872011 1.104683e-06 4.897028e-04
## PGK1            6036.99928     -0.6464248 0.1565218  -4.129935 3.628658e-05 8.153048e-03
## GPR50            107.23642      1.9081133 0.4578166   4.167855 3.074789e-05 7.120976e-03
## BMF             1449.95268      0.6081731 0.1599923   3.801265 1.439591e-04 2.166254e-02
## UNC5B            725.91188      1.2470010 0.2708843   4.603446 4.155569e-06 1.585108e-03
## FZD10           1452.12492     -5.8717934 0.6206858  -9.460170 3.074433e-21 1.260671e-17
## RND3            2668.94662     -1.0237312 0.2790252  -3.668956 2.435428e-04 3.072761e-02
## CLU             2438.39969      0.9569952 0.1931230   4.955366 7.219434e-07 3.383233e-04
## DNAI1             85.97086      0.7937699 0.2272564   3.492839 4.779154e-04 4.693873e-02
## EGR2             183.81068     -1.6163152 0.3922085  -4.121062 3.771305e-05 8.359047e-03
## P4HA1           1803.85468     -0.9187165 0.1918919  -4.787678 1.687221e-06 7.095845e-04
## SSUH2             70.59441     -2.2201533 0.3843751  -5.776007 7.649401e-09 5.702976e-06
## APOE             335.84670      1.6050037 0.4165763   3.852845 1.167535e-04 1.982363e-02
## SPINK5           338.95977      1.3031693 0.3127142   4.167285 3.082486e-05 7.120976e-03
## LMO2             173.60297      2.3075551 0.5840546   3.950923 7.785024e-05 1.451022e-02
## TFCP2           1320.40127     -0.7005710 0.1067600  -6.562109 5.305196e-11 5.438489e-08
## ZFHX2            692.36492      0.6727438 0.1739719   3.866968 1.101968e-04 1.902577e-02
## SPAG8            109.41046      1.0721469 0.2389824   4.486301 7.247021e-06 2.330699e-03
## MNS1             149.14792     -0.8892892 0.2355938  -3.774671 1.602192e-04 2.367492e-02
## LEF1             857.44881      0.9722526 0.2766127   3.514852 4.399992e-04 4.510542e-02
## SLC15A4          124.41296     -4.0253318 0.3978958 -10.116547 4.665860e-24 2.550981e-20
## HDC               57.64489      3.1183735 0.8561961   3.642125 2.703965e-04 3.273311e-02
## CFAP74            57.33016      2.0365413 0.4534864   4.490855 7.093796e-06 2.327049e-03
## RSPO3            346.42227      1.4587272 0.3523141   4.140416 3.466762e-05 7.897476e-03
## TRIM4            168.68946      1.7859980 0.4533840   3.939261 8.173298e-05 1.506275e-02
## IGSF1            215.36251      1.3773355 0.3938709   3.496921 4.706611e-04 4.650472e-02
## VAX1              72.91832      4.6506944 1.0901135   4.266248 1.987878e-05 5.284352e-03
## LRRC4C           121.95019      1.4394951 0.3670378   3.921926 8.784400e-05 1.583316e-02
## GLT1D1            35.03359     -6.4608763 1.2769046  -5.059796 4.197058e-07 2.024710e-04
## TMEM132D         168.74525     -9.3104298 1.2673318  -7.346482 2.034921e-13 2.781399e-10
## ANGPT1            55.85853     -2.2887429 0.4112982  -5.564680 2.626337e-08 1.794882e-05
## GRIA1           1958.45414     -0.7809598 0.2096796  -3.724538 1.956732e-04 2.662048e-02
## B3GNT7            38.35613      1.6018271 0.4039281   3.965624 7.320411e-05 1.380108e-02
## TMSB15B          275.74392     -0.7978565 0.1857422  -4.295505 1.742958e-05 4.845423e-03
## TPPP3            102.76556      1.4693725 0.3687899   3.984308 6.767717e-05 1.321477e-02
## RSPH1             47.87268      1.9430801 0.5208508   3.730589 1.910329e-04 2.655357e-02
## PPP1R32          135.35555      0.9363681 0.2052502   4.562081 5.064903e-06 1.767543e-03
## ABHD6            157.40356      0.9937770 0.2727153   3.644008 2.684248e-04 3.273311e-02
## SERINC5          685.24965      1.0467354 0.2938921   3.561632 3.685574e-04 4.042342e-02
## IFTAP            169.11163      4.2197834 0.5678572   7.431064 1.077277e-13 1.766949e-10
## CRABP1         12001.80107     -1.2840464 0.2808614  -4.571815 4.835183e-06 1.724058e-03
## ZNF667-AS1       234.54796     -1.4857642 0.2558097  -5.808083 6.319222e-09 4.935614e-06
## ZNF558            27.67133     -5.6794358 1.2352324  -4.597868 4.268358e-06 1.591128e-03
## PFKFB3           953.14539     -0.6080256 0.1433679  -4.241017 2.225092e-05 5.614764e-03
## ZNF439           325.88711     -0.8919666 0.2003838  -4.451290 8.535588e-06 2.641523e-03
## DRC3             137.06878      1.0825485 0.2977215   3.636112 2.767843e-04 3.313734e-02
## LRRN3            633.65442     -1.0854341 0.2764544  -3.926268 8.627391e-05 1.572294e-02
## CNTNAP2         4171.45604      0.9935461 0.2676223   3.712494 2.052273e-04 2.736697e-02
## PDE12            480.11478     -1.2114780 0.2024925  -5.982830 2.192939e-09 2.115800e-06
## BNIP3           1246.26202     -1.0472415 0.2984669  -3.508736 4.502414e-04 4.558555e-02
## SOX11           9439.85367     -0.9051936 0.2148164  -4.213801 2.511087e-05 6.184634e-03
## KCTD12           869.92665     -0.8456710 0.2433435  -3.475215 5.104436e-04 4.924880e-02
## H2AW             237.55017     -1.2704323 0.2474902  -5.133263 2.847616e-07 1.459581e-04
## CFAP65           100.52835      1.0091133 0.2464402   4.094759 4.226079e-05 9.002098e-03
## NKX2-5            55.91924     -2.7459226 0.6538525  -4.199605 2.673807e-05 6.355911e-03
## GAS6             527.65113      0.9487736 0.2578042   3.680210 2.330420e-04 2.984389e-02
## PDE4B           1161.27207     -0.7834277 0.2117972  -3.698953 2.164910e-04 2.835340e-02
## ZNF829           136.11596     -1.0374287 0.2569918  -4.036816 5.418143e-05 1.097141e-02
## TPCN1            714.21855      0.6051168 0.1699369   3.560832 3.696813e-04 4.042342e-02
## LINC01551         38.76308      4.6406928 1.2778643   3.631601 2.816689e-04 3.347778e-02
## BCAM             554.21718      0.8381213 0.2368970   3.537915 4.033006e-04 4.240344e-02
## DNAJB13           24.12380      1.8361519 0.5012056   3.663470 2.488212e-04 3.099745e-02
## PCDH18          2951.58289     -0.8586920 0.2236685  -3.839128 1.234720e-04 2.036503e-02
## MYBPC1           121.76197     -2.5123666 0.7005787  -3.586130 3.356213e-04 3.849553e-02
## ZNF471           243.28340     -1.3543080 0.2996731  -4.519285 6.204896e-06 2.120265e-03
## ZNF493           506.98777     -0.5995286 0.1306029  -4.590468 4.422535e-06 1.611965e-03
## ZNF605           961.46814     -0.9817251 0.1317127  -7.453532 9.087419e-14 1.656132e-10
## ZFP28            209.04556     -1.1020145 0.2931105  -3.759723 1.701014e-04 2.423237e-02
## ZNF100           556.84237     -1.4588955 0.1564802  -9.323196 1.128878e-20 3.703170e-17
## CFAP43           213.28265      0.8625323 0.2291546   3.763976 1.672328e-04 2.423237e-02
## ZNF667           174.50297     -1.3977108 0.2371525  -5.893722 3.775915e-09 3.259609e-06
## MT-CYB         45319.46793      0.6870109 0.1414984   4.855257 1.202308e-06 5.189540e-04
## MT-ND2         39999.33168      0.7808431 0.1491730   5.234480 1.654499e-07 9.357618e-05
## MT-ND1         34332.71491      0.7897981 0.1856308   4.254672 2.093556e-05 5.450556e-03
## MT-ATP6        54288.71385      0.7356833 0.1324817   5.553092 2.806598e-08 1.841353e-05
## FANK1             72.93393      1.2667167 0.3298365   3.840438 1.228150e-04 2.036503e-02
## PCDHA4           740.50651     -0.7720398 0.1316070  -5.866254 4.457521e-09 3.655613e-06
## PCDHA2           172.14628     -3.6385853 0.3354445 -10.847057 2.059507e-27 2.814025e-23
## MEG3            5389.42705     -6.8660490 0.9186393  -7.474151 7.770392e-14 1.593125e-10
## MEG9              66.00836     -5.9956704 0.8111506  -7.391562 1.451134e-13 2.163773e-10
## PRR29            103.52019      1.4689771 0.3772792   3.893607 9.876454e-05 1.723336e-02
## MEG8              58.89027     -2.4505888 0.4952216  -4.948469 7.479947e-07 3.407947e-04
## LINC01515        195.86995     -5.0361825 0.4663008 -10.800286 3.431320e-27 2.814025e-23
## MT-ATP8        13072.88599      0.7342644 0.1334619   5.501676 3.761968e-08 2.373223e-05
## SILC1            263.50428     -1.7542583 0.4164477  -4.212433 2.526341e-05 6.184634e-03
## MCIDAS            15.18667      3.7187332 0.8449311   4.401226 1.076408e-05 3.152722e-03
## PCDHA13           47.98728      1.6259670 0.4670627   3.481260 4.990602e-04 4.865408e-02
## TNFRSF6B          22.78767     -3.9356957 1.0288861  -3.825200 1.306657e-04 2.041123e-02
## ZNF585B          278.29547     -1.2186888 0.1733314  -7.030976 2.050933e-12 2.402815e-09
## FZD10-AS1        332.37868     -5.7213380 0.8695262  -6.579834 4.709741e-11 5.149945e-08
## PURPL            103.46331      1.6335988 0.3494943   4.674178 2.951331e-06 1.210193e-03
## LINC02381         54.13587      1.8333424 0.5279725   3.472421 5.157876e-04 4.947338e-02
## PCDHA3            27.07316     -3.1293753 0.7058229  -4.433655 9.264873e-06 2.762954e-03
## BLOC1S5-TXNDC5    19.56246      4.8548809 1.2662889   3.833944 1.261048e-04 2.041123e-02
## TXNIP           9764.81344     -0.9063041 0.2208495  -4.103718 4.065628e-05 8.891257e-03
## ZNF790-AS1       123.79130     -0.9942417 0.2322395  -4.281104 1.859682e-05 5.083751e-03
## MIR924HG          35.75603     -4.8224722 0.8137372  -5.926326 3.097868e-09 2.822846e-06
## LINC02893         57.59384      1.3085359 0.3644242   3.590695 3.297976e-04 3.836412e-02
## LHX1              43.69816      3.8405836 0.8273769   4.641879 3.452545e-06 1.381186e-03
## LHX1-DT           13.31591      3.8961246 1.0909737   3.571236 3.553003e-04 3.991532e-02
## ZNF229            44.84718     -3.3817807 0.8320010  -4.064635 4.810762e-05 9.988115e-03
## BLACAT1         1298.36493      1.2782732 0.2882446   4.434682 9.220814e-06 2.762954e-03
## 
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 17781 rows and 5 columns
##                baseMean log2FoldChange     lfcSE     pvalue      padj
##               <numeric>      <numeric> <numeric>  <numeric> <numeric>
## TSPAN6       1899.95350     -0.0010493 0.0615334 0.97617617 0.9969430
## TNMD            1.40474     -0.0106537 0.1642036 0.22254342        NA
## DPM1          753.98864     -0.0403886 0.0625618 0.25080293 0.7661892
## SCYL3         324.26243     -0.0221282 0.0671931 0.47876749 0.8878547
## C1orf112      606.44497     -0.1419023 0.1090634 0.00127186 0.0876281
## ...                 ...            ...       ...        ...       ...
## C8orf44       219.88820     0.02259276 0.0723834   0.393687  0.848049
## C8orf44-SGK3    6.72668     0.00151019 0.1155706   0.857683  0.981561
## NPBWR1          3.20140     0.00222092 0.1169012   0.790540        NA
## PDCD6-AHRR     25.30042    -0.00299776 0.1623399   0.620577  0.938008
## LNCDAT          7.67620    -0.01034970 0.1149481   0.355371  0.825025
## 
## $AR$DEGsAshr
##                   baseMean log2FoldChange     lfcSE       pvalue         padj
## NRXN3            125.92310      0.9126397 0.5902348 6.312865e-05 1.247513e-02
## DSG2             537.93484      0.8359665 0.5148227 7.102070e-05 1.354513e-02
## UBE2T            701.97049     -0.9806010 0.1121235 4.697111e-19 1.284034e-15
## ZNF506           590.46712     -1.0261038 0.1415734 7.173113e-14 1.593125e-10
## HSD17B14         169.46894      0.6351254 0.4204949 1.241619e-04 2.036503e-02
## BMP7            1638.74041      0.8779839 0.2125229 1.104683e-06 4.897028e-04
## GPR50            107.23642      1.1785707 0.7233921 3.074789e-05 7.120976e-03
## UNC5B            725.91188      1.0421259 0.3104101 4.155569e-06 1.585108e-03
## FZD10           1452.12492     -5.6911650 0.6131068 3.074433e-21 1.260671e-17
## CLU             2438.39969      0.8695582 0.2018081 7.219434e-07 3.383233e-04
## EGR2             183.81068     -1.0327598 0.5921705 3.771305e-05 8.359047e-03
## P4HA1           1803.85468     -0.8278875 0.2106695 1.687221e-06 7.095845e-04
## SSUH2             70.59441     -2.0000403 0.4445010 7.649401e-09 5.702976e-06
## APOE             335.84670      0.7949383 0.6497645 1.167535e-04 1.982363e-02
## SPINK5           338.95977      0.9377023 0.4450286 3.082486e-05 7.120976e-03
## LMO2             173.60297      1.0346647 0.9890821 7.785024e-05 1.451022e-02
## TFCP2           1320.40127     -0.6806554 0.1057329 5.305196e-11 5.438489e-08
## SPAG8            109.41046      0.9043269 0.2888817 7.247021e-06 2.330699e-03
## SLC15A4          124.41296     -3.9706744 0.3958319 4.665860e-24 2.550981e-20
## HDC               57.64489      0.6861777 1.1958326 2.703965e-04 3.273311e-02
## CFAP74            57.33016      1.5071054 0.6542686 7.093796e-06 2.327049e-03
## RSPO3            346.42227      0.9886676 0.5156740 3.466762e-05 7.897476e-03
## TRIM4            168.68946      0.9095277 0.7202042 8.173298e-05 1.506275e-02
## VAX1              72.91832      2.9306561 2.0839005 1.987878e-05 5.284352e-03
## LRRC4C           121.95019      0.8265490 0.5696149 8.784400e-05 1.583316e-02
## GLT1D1            35.03359     -5.5941161 1.4423473 4.197058e-07 2.024710e-04
## TMEM132D         168.74525     -8.4980779 1.3078588 2.034921e-13 2.781399e-10
## ANGPT1            55.85853     -2.0493504 0.4839509 2.626337e-08 1.794882e-05
## B3GNT7            38.35613      0.8994310 0.6301310 7.320411e-05 1.380108e-02
## TMSB15B          275.74392     -0.6633349 0.2608410 1.742958e-05 4.845423e-03
## TPPP3            102.76556      0.8831230 0.5675211 6.767717e-05 1.321477e-02
## RSPH1             47.87268      0.6899528 0.7789260 1.910329e-04 2.655357e-02
## PPP1R32          135.35555      0.8181424 0.2442201 5.064903e-06 1.767543e-03
## IFTAP            169.11163      4.1039970 0.5630433 1.077277e-13 1.766949e-10
## CRABP1         12001.80107     -1.0600735 0.3269466 4.835183e-06 1.724058e-03
## ZNF667-AS1       234.54796     -1.3219752 0.2574071 6.319222e-09 4.935614e-06
## ZNF558            27.67133     -4.4452292 1.9417370 4.268358e-06 1.591128e-03
## ZNF439           325.88711     -0.7675315 0.2534955 8.535588e-06 2.641523e-03
## LRRN3            633.65442     -0.7147027 0.4298763 8.627391e-05 1.572294e-02
## PDE12            480.11478     -1.1105677 0.1986193 2.192939e-09 2.115800e-06
## SOX11           9439.85367     -0.7254751 0.3044308 2.511087e-05 6.184634e-03
## H2AW             237.55017     -1.1173641 0.2494239 2.847616e-07 1.459581e-04
## CFAP65           100.52835      0.7539248 0.3633011 4.226079e-05 9.002098e-03
## NKX2-5            55.91924     -1.6501242 1.2052336 2.673807e-05 6.355911e-03
## ZNF829           136.11596     -0.7458310 0.3869659 5.418143e-05 1.097141e-02
## LINC01551         38.76308      0.8205709 1.6643270 2.816689e-04 3.347778e-02
## DNAJB13           24.12380      0.6142944 0.7224778 2.488212e-04 3.099745e-02
## ZNF471           243.28340     -1.0921236 0.3596737 6.204896e-06 2.120265e-03
## ZNF605           961.46814     -0.9425028 0.1297721 9.087419e-14 1.656132e-10
## ZFP28            209.04556     -0.6212233 0.4642478 1.701014e-04 2.423237e-02
## ZNF100           556.84237     -1.3952506 0.1573433 1.128878e-20 3.703170e-17
## ZNF667           174.50297     -1.2558979 0.2358341 3.775915e-09 3.259609e-06
## MT-CYB         45319.46793      0.6348461 0.1659696 1.202308e-06 5.189540e-04
## MT-ND2         39999.33168      0.7349800 0.1539092 1.654499e-07 9.357618e-05
## MT-ND1         34332.71491      0.6476628 0.2663892 2.093556e-05 5.450556e-03
## MT-ATP6        54288.71385      0.7023052 0.1338287 2.806598e-08 1.841353e-05
## FANK1             72.93393      0.7230640 0.5158660 1.228150e-04 2.036503e-02
## PCDHA4           740.50651     -0.7391587 0.1305034 4.457521e-09 3.655613e-06
## PCDHA2           172.14628     -3.6022444 0.3347542 2.059507e-27 2.814025e-23
## MEG3            5389.42705     -6.4386068 0.9011922 7.770392e-14 1.593125e-10
## MEG9              66.00836     -5.6885513 0.7948997 1.451134e-13 2.163773e-10
## PRR29            103.52019      0.8096358 0.5873932 9.876454e-05 1.723336e-02
## MEG8              58.89027     -2.0978304 0.6513969 7.479947e-07 3.407947e-04
## LINC01515        195.86995     -4.9453502 0.4625909 3.431320e-27 2.814025e-23
## MT-ATP8        13072.88599      0.7001340 0.1353783 3.761968e-08 2.373223e-05
## SILC1            263.50428     -1.1546873 0.6259759 2.526341e-05 6.184634e-03
## MCIDAS            15.18667      2.7491262 1.5254740 1.076408e-05 3.152722e-03
## TNFRSF6B          22.78767     -1.2092311 1.7232238 1.306657e-04 2.041123e-02
## ZNF585B          278.29547     -1.1431862 0.1709485 2.050933e-12 2.402815e-09
## FZD10-AS1        332.37868     -5.3834598 0.8492106 4.709741e-11 5.149945e-08
## PURPL            103.46331      1.3073952 0.4144333 2.951331e-06 1.210193e-03
## PCDHA3            27.07316     -2.3426023 1.2403810 9.264873e-06 2.762954e-03
## BLOC1S5-TXNDC5    19.56246      1.3727224 2.0578874 1.261048e-04 2.041123e-02
## TXNIP           9764.81344     -0.6922104 0.3288879 4.065628e-05 8.891257e-03
## ZNF790-AS1       123.79130     -0.8053930 0.3135949 1.859682e-05 5.083751e-03
## MIR924HG          35.75603     -4.5591386 0.8042174 3.097868e-09 2.822846e-06
## LHX1              43.69816      3.2488715 1.2653518 3.452545e-06 1.381186e-03
## LHX1-DT           13.31591      0.6569610 1.3712051 3.553003e-04 3.991532e-02
## ZNF229            44.84718     -1.6924821 1.5933962 4.810762e-05 9.988115e-03
## BLACAT1         1298.36493      1.0242981 0.3576873 9.220814e-06 2.762954e-03

DEA for Day50

DEAList_day50_HT <- readRDS(paste0(params$InputFolder, 'day50/Output/Savings/day50CbO.DEAList_HT.rds'))
DEAList_day50_AR <- readRDS(paste0(params$InputFolder, 'day50/Output/Savings/day50CbO.DEAList_AR.rds'))

DEAList_day50_HT
## $dds
## class: DESeqDataSet 
## dim: 17673 14 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17673): TSPAN6 TNMD ... NPBWR1 PDCD6-AHRR
## rowData names(47): Gene EnsGene ... deviance maxCooks
## colnames(14): OLE_010 OLE_011 ... OLE_048 OLE_049
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 17673 rows and 6 columns
##                baseMean log2FoldChange     lfcSE      stat      pvalue       padj
##               <numeric>      <numeric> <numeric> <numeric>   <numeric>  <numeric>
## TSPAN6       1022.69733      -0.113571 0.1088076  -1.04377 0.296589803 0.46422519
## TNMD            7.74747       2.675421 0.9693185   2.76011 0.005778269 0.02123805
## DPM1          566.77011      -0.122239 0.0911219  -1.34149 0.179763013 0.32447589
## SCYL3         326.10166      -0.120111 0.0949914  -1.26444 0.206072526 0.35935167
## C1orf112      220.67316      -0.487005 0.1295828  -3.75825 0.000171104 0.00106128
## ...                 ...            ...       ...       ...         ...        ...
## LINC01949       6.08511      -0.533526  0.608744 -0.876439    0.380792   0.553295
## C8orf44       175.25242      -0.221174  0.171898 -1.286660    0.198213   0.348982
## C8orf44-SGK3   11.64862      -0.974339  0.604945 -1.610624    0.107262   0.221581
## NPBWR1          3.66410       1.095843  1.038395  1.055324    0.291277   0.458602
## PDCD6-AHRR     40.02742       1.661350  2.417512  0.687215    0.491947   0.657452
## 
## $HT$DEGs
##              baseMean log2FoldChange      lfcSE       stat       pvalue         padj
## TNMD         7.747472      2.6754212 0.96931846   2.760106 5.778269e-03 2.123805e-02
## STPG1       65.812213     -0.6235108 0.21717451  -2.871013 4.091587e-03 1.599170e-02
## HS3ST1      14.255409      3.0124979 0.81654757   3.689311 2.248622e-04 1.341895e-03
## HECW1      487.012064      0.8998175 0.14022555   6.416930 1.390502e-10 3.824984e-09
## TMEM176A    25.491782     -2.0059545 0.72412383  -2.770182 5.602504e-03 2.071062e-02
## KLHL13     805.517717      0.8119393 0.14104425   5.756628 8.581068e-09 1.547450e-07
## CYP26B1   2066.779889      1.3435384 0.35285664   3.807604 1.403197e-04 8.936937e-04
## PDK4        24.639527     -1.9826830 0.55612120  -3.565200 3.635795e-04 2.038624e-03
## SLC25A13   685.642382     -0.9047285 0.13729488  -6.589674 4.407920e-11 1.337815e-09
## SKAP2       64.500162      1.7490964 0.32458828   5.388662 7.098432e-08 1.020878e-06
## MCUB        78.457896     -1.2395485 0.33726890  -3.675253 2.376140e-04 1.406360e-03
## PRKAR2B   2149.632951      0.7112178 0.09503448   7.483786 7.221125e-14 3.409867e-12
## GCFC2      139.052502      0.6269703 0.23428556   2.676094 7.448566e-03 2.628460e-02
## CROT       195.452210     -0.6264758 0.14956193  -4.188739 2.805093e-05 2.166322e-04
## SOX8       440.265741      1.6229314 0.26294019   6.172246 6.732680e-10 1.591778e-08
## ITGA3      260.507308      0.6724120 0.16871128   3.985578 6.731607e-05 4.702086e-04
## ITGA2B     134.019740      0.9688376 0.18851132   5.139413 2.755975e-07 3.492227e-06
## CRLF1       18.764256      3.6201803 0.63811239   5.673264 1.401018e-08 2.378025e-07
## CACNG3      49.962057      1.8704266 0.57996491   3.225069 1.259425e-03 5.851430e-03
## TMEM132A  3655.584391      0.7894159 0.12498370   6.316151 2.681579e-10 6.905165e-09
## TAC1       182.897862     -0.7656924 0.31097869  -2.462202 1.380869e-02 4.389298e-02
## CACNA1G    772.587817      1.0883896 0.23693178   4.593683 4.354898e-06 4.119562e-05
## ALDH3B1     57.244239      1.0738323 0.41529878   2.585686 9.718541e-03 3.280528e-02
## SCIN        13.585603      1.8413892 0.67269777   2.737320 6.194198e-03 2.255157e-02
## DNAH9       22.899935      3.2366585 0.67390785   4.802821 1.564461e-06 1.666386e-05
## GAS7       281.832223      0.9759929 0.24954658   3.911065 9.188997e-05 6.172299e-04
## TKTL1      293.479618      1.8058084 0.18469186   9.777412 1.407639e-22 1.793705e-20
## PAX6      1451.617069     -0.6093800 0.18362219  -3.318662 9.044985e-04 4.432964e-03
## BAIAP3    1063.001823      0.7271966 0.12300230   5.912057 3.378614e-09 6.768946e-08
## E2F2       269.826168     -1.1122790 0.23616769  -4.709700 2.480815e-06 2.520078e-05
## SYN1       721.454609      0.6161452 0.10768182   5.721906 1.053358e-08 1.851957e-07
## CAMK1G     114.341248      0.6594771 0.22834891   2.888024 3.876707e-03 1.531070e-02
## NFIX       115.808109      3.5142409 0.72407042   4.853452 1.213308e-06 1.325765e-05
## ST3GAL1    135.727967      1.2456746 0.14923637   8.346991 7.002403e-17 5.098809e-15
## TENM1     1133.760447      0.9120483 0.14270628   6.391087 1.647102e-10 4.398194e-09
## MLXIPL      59.548735      0.5988461 0.23820486   2.513996 1.193718e-02 3.903570e-02
## CD9        193.882636      2.1480194 0.34470316   6.231505 4.619761e-10 1.124445e-08
## NCAPD2    2723.707691     -0.5870980 0.09841789  -5.965358 2.440977e-09 5.115130e-08
## LRRC23     227.418610      0.7976638 0.20306072   3.928204 8.558276e-05 5.795816e-04
## SYT7       965.302871      0.6732342 0.20154729   3.340329 8.367922e-04 4.143317e-03
## ANLN       559.936125     -1.0618559 0.21650067  -4.904631 9.360299e-07 1.041837e-05
## BRCA1      621.295024     -1.0916569 0.20568637  -5.307386 1.112087e-07 1.533211e-06
## EHD3       342.978006      0.6221504 0.10472630   5.940728 2.837596e-09 5.847270e-08
## MAMLD1     291.210473      0.7119429 0.12528880   5.682414 1.328066e-08 2.269762e-07
## TACC3     1159.637511     -0.9861690 0.14372034  -6.861722 6.803551e-12 2.386752e-10
## MTMR11     113.993913      0.8724068 0.20788453   4.196593 2.709597e-05 2.100059e-04
## STMN4     4436.952174      0.7085134 0.11733632   6.038313 1.557335e-09 3.411961e-08
## ATP1A2    2625.086059      2.1834367 0.28790891   7.583776 3.356399e-14 1.661897e-12
## ZNF582     118.445905     -0.9380685 0.15324260  -6.121461 9.272147e-10 2.122673e-08
## SYT13     1975.687935      0.6686761 0.13805416   4.843578 1.275218e-06 1.387290e-05
## CD74        15.453855     -1.5049913 0.51523903  -2.920958 3.489574e-03 1.398197e-02
## ADGRA2      66.488811      0.9601402 0.35853911   2.677923 7.408022e-03 2.616888e-02
## PLEKHB1     34.543679      1.0912017 0.37321336   2.923801 3.457855e-03 1.388430e-02
## CPS1       590.870863     -1.7230416 0.24826487  -6.940336 3.911689e-12 1.418192e-10
## GRAMD1B    587.202951      1.2164202 0.16141581   7.535942 4.848213e-14 2.346914e-12
## DEPDC1     307.825618     -1.0787636 0.23424472  -4.605284 4.119025e-06 3.917821e-05
## TYMP        19.180540     -1.4559062 0.45598309  -3.192895 1.408540e-03 6.462801e-03
## FAS        113.681992     -1.6531942 0.25540643  -6.472798 9.620457e-11 2.719780e-09
## VRK2        38.370869     -2.9150557 0.51744529  -5.633553 1.765338e-08 2.941665e-07
## TNFRSF1B    20.531579     -1.8261562 0.55502612  -3.290217 1.001103e-03 4.816521e-03
## ARHGAP31    82.086978      0.8215074 0.24312055   3.379013 7.274668e-04 3.678728e-03
## LRRC7      771.709600      0.6573541 0.16399449   4.008391 6.113373e-05 4.326041e-04
## TMSB10   12568.018286      0.6901659 0.05933620  11.631448 2.852187e-31 7.061199e-29
## DEPDC1B    351.717126     -0.9176015 0.19189528  -4.781783 1.737476e-06 1.833767e-05
## FLT4       137.237414     -0.6587485 0.20226701  -3.256826 1.126654e-03 5.337593e-03
## TNC        555.584575      2.1903828 0.45409344   4.823639 1.409625e-06 1.515512e-05
## DSG2       401.819038     -2.1621773 0.18610932 -11.617781 3.347188e-31 8.169969e-29
## PREX2      591.448627     -1.0993578 0.17898198  -6.142282 8.134447e-10 1.887148e-08
## ANO2        35.165313     -1.3376513 0.33088684  -4.042625 5.285616e-05 3.797667e-04
## COL9A2     112.687942      0.8091058 0.20368525   3.972334 7.117196e-05 4.927727e-04
## NEDD4L    3733.242616      0.8386599 0.06638800  12.632704 1.394039e-36 4.930347e-34
## RAD51      101.135116     -1.3701430 0.30302240  -4.521590 6.137692e-06 5.586460e-05
## POLQ       248.635228     -1.2305640 0.23194767  -5.305352 1.124560e-07 1.547944e-06
## MSMO1     7891.326281      0.6416935 0.11605302   5.529313 3.214872e-08 5.011065e-07
## NRIP2       10.076169      1.4961962 0.49587145   3.017307 2.550317e-03 1.072482e-02
## ENTPD2      25.312397      2.4646037 0.65198089   3.780178 1.567164e-04 9.865220e-04
## OPN3       158.297689     -0.6030563 0.20047344  -3.008160 2.628344e-03 1.098895e-02
## HHAT       167.638967     -0.7232529 0.18880865  -3.830613 1.278244e-04 8.241060e-04
## FOXC1       23.672777      2.1787810 0.59751912   3.646379 2.659619e-04 1.552415e-03
## GYG2       165.837279     -0.7645464 0.28836148  -2.651347 8.017142e-03 2.801150e-02
## F7          21.969485      2.1523640 0.49449327   4.352666 1.344920e-05 1.123252e-04
## RASGRF1     94.140182      1.4443405 0.33663671   4.290502 1.782696e-05 1.444325e-04
## CAMK2B     626.022451      0.6163167 0.17732267   3.475679 5.095617e-04 2.720488e-03
## PARP12      24.405251     -1.6764611 0.35854180  -4.675776 2.928443e-06 2.914986e-05
## YBX3      1001.227899     -0.6815838 0.12168804  -5.601075 2.130269e-08 3.486077e-07
## RIMBP2     473.676494      0.8109779 0.11555218   7.018283 2.246110e-12 8.517523e-11
## MPC1       425.661915      0.8267666 0.19554097   4.228099 2.356739e-05 1.859849e-04
## PRDM6       61.628043     -0.8184650 0.29984987  -2.729583 6.341452e-03 2.300071e-02
## GUCY1B1    398.428899      1.1423971 0.15469321   7.384921 1.525441e-13 6.829161e-12
## SEZ6       591.699557      1.0348366 0.17364541   5.959481 2.530397e-09 5.283347e-08
## NGFR      1703.309930      1.4665600 0.17306752   8.473918 2.372745e-17 1.795619e-15
## EYA2        77.523749     -0.7847873 0.31087927  -2.524412 1.158921e-02 3.805247e-02
## CNN2      1201.727345     -0.7700051 0.16427528  -4.687285 2.768533e-06 2.781373e-05
## ABCA7      347.950748      0.6593548 0.11433941   5.766645 8.086490e-09 1.465888e-07
## HMG20B     779.189544     -1.1079623 0.16652830  -6.653298 2.865977e-11 9.014045e-10
## MCM10      400.286506     -1.3658449 0.28604522  -4.774927 1.797728e-06 1.890451e-05
## ANKRD44    460.609498      0.9615212 0.13226569   7.269619 3.605022e-13 1.531251e-11
## PACC1      356.175655      0.5991247 0.11733555   5.106080 3.289105e-07 4.124471e-06
## TLE2        35.801382      1.1639920 0.39781885   2.925935 3.434229e-03 1.380222e-02
## ME1          9.541013     -3.0033114 0.69635702  -4.312890 1.611341e-05 1.317195e-04
## NGEF        71.459698      1.6592032 0.27583453   6.015212 1.796516e-09 3.891702e-08
## ASPM      1362.616996     -1.3929710 0.23659795  -5.887503 3.920750e-09 7.765325e-08
## FGFR2     1275.552836     -0.9072640 0.14481665  -6.264915 3.730293e-10 9.301222e-09
## KIF26A     285.174118      1.4354425 0.28827657   4.979394 6.378378e-07 7.388856e-06
## PFKP      1032.139835     -0.6702403 0.14146084  -4.737992 2.158461e-06 2.229210e-05
## PHKA1      185.421052     -1.0811016 0.13716143  -7.881965 3.222728e-15 1.932522e-13
## PRKCZ      372.260418      1.0077724 0.17584646   5.730979 9.985254e-09 1.770716e-07
## ATP2B3     174.188111      1.2811794 0.19071394   6.717807 1.844796e-11 6.054983e-10
## COASY      885.297873      0.6382370 0.13156212   4.851222 1.227033e-06 1.338231e-05
## ACSL4     1428.621028      0.7213031 0.05076057  14.209910 7.952779e-46 4.752471e-43
## PRR11     1159.566332     -0.8051860 0.16711847  -4.818055 1.449642e-06 1.553636e-05
## REEP1     1338.125830      0.7891907 0.10385109   7.599253 2.978449e-14 1.504855e-12
## RORA      1277.590519      0.8789024 0.16588804   5.298166 1.169714e-07 1.603729e-06
## TGFBR3     108.485202     -1.0688853 0.38320278  -2.789346 5.281455e-03 1.975558e-02
## PTPN3      284.712207      0.5976931 0.13018953   4.590946 4.412415e-06 4.165330e-05
## FGF10       28.238833     -2.8635967 0.90353457  -3.169327 1.527923e-03 6.900937e-03
## CHAT        23.974671      1.5100323 0.41142935   3.670211 2.423508e-04 1.427095e-03
## NCK2      1093.838024      0.5868832 0.08729080   6.723312 1.776400e-11 5.863812e-10
## TRIP13     237.668862     -1.1084049 0.20326797  -5.452924 4.954816e-08 7.408710e-07
## SPEG      1382.546481      0.7726248 0.11783072   6.557074 5.487380e-11 1.633957e-09
## LNX1       111.678560      1.2856622 0.34964425   3.677058 2.359393e-04 1.399325e-03
## HMMR       371.538865     -0.7340296 0.17332471  -4.234997 2.285548e-05 1.807784e-04
## TRNT1      314.267168     -0.8151645 0.14322767  -5.691390 1.260094e-08 2.170719e-07
## EVC        303.514220     -0.8403210 0.18859958  -4.455582 8.366581e-06 7.341410e-05
## NDE1       552.722825     -0.7507275 0.16175192  -4.641228 3.463455e-06 3.372005e-05
## IRAG1       95.810082     -1.0323551 0.19381558  -5.326481 1.001336e-07 1.397981e-06
## MCM2      1870.272466     -1.0721492 0.15101591  -7.099578 1.251388e-12 4.996903e-11
## GSDMB      606.090468      0.6123023 0.09543013   6.416236 1.396845e-10 3.836342e-09
## ST6GAL1    379.864278      1.4405371 0.25147092   5.728444 1.013559e-08 1.794175e-07
## GLI2      1511.655055     -0.6610411 0.08016228  -8.246286 1.633928e-16 1.146396e-14
## PPP2R2C    289.889331      1.3513444 0.21595847   6.257427 3.913802e-10 9.648108e-09
## TEAD2     1219.154415     -0.7036819 0.12731676  -5.527017 3.257218e-08 5.067108e-07
## CA12       508.558506      1.2588252 0.22212320   5.667239 1.451172e-08 2.455870e-07
## ENO1     10554.040630     -0.7894907 0.10384467  -7.602611 2.902145e-14 1.474903e-12
## SEMA3A     548.021439     -1.5861311 0.15857805 -10.002211 1.490321e-23 2.002114e-21
## GTSE1      486.670135     -1.2186529 0.16964689  -7.183468 6.796513e-13 2.817789e-11
## ZNF37A     110.743181      4.2526613 0.34021059  12.500085 7.457127e-36 2.485231e-33
## CACNG5     225.061635      0.9417253 0.24602984   3.827687 1.293530e-04 8.324127e-04
## WDR62      333.109321     -0.9516515 0.15304493  -6.218118 5.031529e-10 1.212746e-08
## ARHGAP15    22.274407      1.3577565 0.40287511   3.370167 7.512258e-04 3.787087e-03
## PAX2       324.551902      1.9790411 0.45169648   4.381352 1.179454e-05 1.000976e-04
## FMO4        35.197717     -0.7851708 0.28304461  -2.774018 5.536866e-03 2.053807e-02
## RGS11      120.008733     -1.3569287 0.31337098  -4.330103 1.490395e-05 1.231691e-04
## SPAG5      898.227860     -0.6791081 0.12065460  -5.628530 1.817515e-08 3.022796e-07
## TPD52      307.232828     -1.5397031 0.17665671  -8.715792 2.887332e-18 2.338199e-16
## ACACB      238.611693     -0.7798707 0.16863483  -4.624612 3.752997e-06 3.609292e-05
## MCAM       551.118702      0.6415512 0.15742417   4.075303 4.595442e-05 3.363134e-04
## GPC4      2569.023914     -0.6330591 0.15807664  -4.004761 6.208026e-05 4.387646e-04
## MBNL3      331.883748     -0.8409148 0.17297075  -4.861602 1.164398e-06 1.276345e-05
## STXBP2      91.913518      0.6911857 0.18179306   3.802047 1.435058e-04 9.119747e-04
## NAALAD2    669.783603     -0.5982613 0.21106014  -2.834554 4.588975e-03 1.755949e-02
## SLC25A43    46.151083     -1.1898470 0.29051633  -4.095629 4.210240e-05 3.106150e-04
## NEBL       525.999884      0.7665189 0.13769530   5.566777 2.594948e-08 4.140925e-07
## ADCY2      433.464629      0.9056368 0.18779281   4.822532 1.417476e-06 1.522930e-05
## RBFOX1      50.519246      4.4797115 0.64294145   6.967526 3.225621e-12 1.191898e-10
## SLC1A3    2053.191508      0.8388029 0.31104409   2.696733 7.002335e-03 2.494870e-02
## LXN          7.299635     -1.8929005 0.77761417  -2.434241 1.492304e-02 4.681946e-02
## FDFT1    14390.391928      0.6333230 0.12897079   4.910593 9.080144e-07 1.013258e-05
## OPHN1      718.035736      0.8931493 0.09058243   9.860072 6.200465e-23 8.202600e-21
## EPB41L2    901.360735     -0.9322259 0.13060172  -7.137930 9.474693e-13 3.845350e-11
## EPHA6       69.840411     -0.9409610 0.36607072  -2.570435 1.015709e-02 3.404686e-02
## SLC4A4     182.442551      1.4920638 0.17395112   8.577489 9.696656e-18 7.569507e-16
## SESN1      883.220023     -0.8406157 0.08535653  -9.848289 6.972073e-23 9.084664e-21
## CHRNA3     507.218051     -0.7168320 0.26588050  -2.696068 7.016325e-03 2.499340e-02
## KCNN2       59.370934      0.7196554 0.26186449   2.748198 5.992388e-03 2.193665e-02
## NDC80      394.130899     -1.1402453 0.23019798  -4.953325 7.295614e-07 8.323435e-06
##  [ reached 'max' / getOption("max.print") -- omitted 2036 rows ]
## 
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT 
## Wald test p-value: Genotype HT vs WT 
## DataFrame with 17673 rows and 5 columns
##                baseMean log2FoldChange     lfcSE      pvalue       padj
##               <numeric>      <numeric> <numeric>   <numeric>  <numeric>
## TSPAN6       1022.69733     -0.0835855 0.0948219 0.296589803 0.46422519
## TNMD            7.74747      0.6594355 0.8028949 0.005778269 0.02123805
## DPM1          566.77011     -0.0970572 0.0825753 0.179763013 0.32447589
## SCYL3         326.10166     -0.0938139 0.0853611 0.206072526 0.35935167
## C1orf112      220.67316     -0.4070108 0.1358880 0.000171104 0.00106128
## ...                 ...            ...       ...         ...        ...
## LINC01949       6.08511      -0.109027  0.296977    0.380792   0.553295
## C8orf44       175.25242      -0.130464  0.139202    0.198213   0.348982
## C8orf44-SGK3   11.64862      -0.244396  0.379235    0.107262   0.221581
## NPBWR1          3.66410       0.124427  0.383416    0.291277   0.458602
## PDCD6-AHRR     40.02742       0.051861  0.441572    0.491947   0.657452
## 
## $HT$DEGsAshr
##              baseMean log2FoldChange      lfcSE       pvalue         padj
## TNMD         7.747472      0.6594355 0.80289494 5.778269e-03 2.123805e-02
## HS3ST1      14.255409      1.5775906 1.04692569 2.248622e-04 1.341895e-03
## HECW1      487.012064      0.8577632 0.14219908 1.390502e-10 3.824984e-09
## TMEM176A    25.491782     -0.6954230 0.66416959 5.602504e-03 2.071062e-02
## KLHL13     805.517717      0.7645500 0.14674769 8.581068e-09 1.547450e-07
## CYP26B1   2066.779889      1.0236067 0.37810526 1.403197e-04 8.936937e-04
## PDK4        24.639527     -1.1884434 0.61408332 3.635795e-04 2.038624e-03
## SLC25A13   685.642382     -0.8647643 0.13886573 4.407920e-11 1.337815e-09
## SKAP2       64.500162      1.4927186 0.32411353 7.098432e-08 1.020878e-06
## MCUB        78.457896     -0.9387770 0.36807050 2.376140e-04 1.406360e-03
## PRKAR2B   2149.632951      0.6881279 0.09786769 7.221125e-14 3.409867e-12
## SOX8       440.265741      1.4525329 0.26028651 6.732680e-10 1.591778e-08
## ITGA2B     134.019740      0.8883232 0.19395976 2.755975e-07 3.492227e-06
## CRLF1       18.764256      3.2687180 0.74943605 1.401018e-08 2.378025e-07
## CACNG3      49.962057      0.9744220 0.62360788 1.259425e-03 5.851430e-03
## TMEM132A  3655.584391      0.7526071 0.12917353 2.681579e-10 6.905165e-09
## CACNA1G    772.587817      0.9568484 0.24483854 4.354898e-06 4.119562e-05
## SCIN        13.585603      0.6783636 0.62486638 6.194198e-03 2.255157e-02
## DNAH9       22.899935      2.5908544 0.86599458 1.564461e-06 1.666386e-05
## GAS7       281.832223      0.8087028 0.27447284 9.188997e-05 6.172299e-04
## TKTL1      293.479618      1.7205352 0.18640894 1.407639e-22 1.793705e-20
## BAIAP3    1063.001823      0.6865672 0.12913628 3.378614e-09 6.768946e-08
## E2F2       269.826168     -0.9831442 0.24174948 2.480815e-06 2.520078e-05
## NFIX       115.808109      2.8887576 0.93975799 1.213308e-06 1.325765e-05
## ST3GAL1    135.727967      1.1939812 0.14743035 7.002403e-17 5.098809e-15
## TENM1     1133.760447      0.8686156 0.14449447 1.647102e-10 4.398194e-09
## CD9        193.882636      1.8810596 0.36461599 4.619761e-10 1.124445e-08
## LRRC23     227.418610      0.6714735 0.22650427 8.558276e-05 5.795816e-04
## ANLN       559.936125     -0.9549735 0.22131150 9.360299e-07 1.041837e-05
## BRCA1      621.295024     -0.9974702 0.20673560 1.112087e-07 1.533211e-06
## MAMLD1     291.210473      0.6677541 0.13234844 1.328066e-08 2.269762e-07
## TACC3     1159.637511     -0.9428606 0.14361740 6.803551e-12 2.386752e-10
## MTMR11     113.993913      0.7550547 0.22737914 2.709597e-05 2.100059e-04
## STMN4     4436.952174      0.6704508 0.12313029 1.557335e-09 3.411961e-08
## ATP1A2    2625.086059      2.0042894 0.30365187 3.356399e-14 1.661897e-12
## ZNF582     118.445905     -0.8876987 0.15508834 9.272147e-10 2.122673e-08
## SYT13     1975.687935      0.6058266 0.14903464 1.275218e-06 1.387290e-05
## CD74        15.453855     -0.7604955 0.53808237 3.489574e-03 1.398197e-02
## PLEKHB1     34.543679      0.6644009 0.40962244 3.457855e-03 1.388430e-02
## CPS1       590.870863     -1.5694256 0.24846764 3.911689e-12 1.418192e-10
## GRAMD1B    587.202951      1.1570221 0.15919869 4.848213e-14 2.346914e-12
## DEPDC1     307.825618     -0.9502479 0.24225063 4.119025e-06 3.917821e-05
## TYMP        19.180540     -0.8756475 0.49787983 1.408540e-03 6.462801e-03
## FAS        113.681992     -1.4914442 0.25370530 9.620457e-11 2.719780e-09
## VRK2        38.370869     -2.5228336 0.61279819 1.765338e-08 2.941665e-07
## TNFRSF1B    20.531579     -1.0042605 0.60188594 1.001103e-03 4.816521e-03
## ARHGAP31    82.086978      0.6269348 0.27543921 7.274668e-04 3.678728e-03
## TMSB10   12568.018286      0.6814710 0.06005098 2.852187e-31 7.061199e-29
## DEPDC1B    351.717126     -0.8290529 0.20208592 1.737476e-06 1.833767e-05
## TNC        555.584575      1.7224760 0.48778992 1.409625e-06 1.515512e-05
## DSG2       401.819038     -2.0897213 0.19127313 3.347188e-31 8.169969e-29
## PREX2      591.448627     -1.0295104 0.17768259 8.134447e-10 1.887148e-08
## ANO2        35.165313     -1.0652944 0.34692296 5.285616e-05 3.797667e-04
## COL9A2     112.687942      0.6846407 0.22666046 7.117196e-05 4.927727e-04
## NEDD4L    3733.242616      0.8299438 0.06650525 1.394039e-36 4.930347e-34
## RAD51      101.135116     -1.1506359 0.30577942 6.137692e-06 5.586460e-05
## POLQ       248.635228     -1.1077426 0.22994263 1.124560e-07 1.547944e-06
## MSMO1     7891.326281      0.5969924 0.12319651 3.214872e-08 5.011065e-07
## NRIP2       10.076169      0.8057117 0.52863101 2.550317e-03 1.072482e-02
## ENTPD2      25.312397      1.4643931 0.76832909 1.567164e-04 9.865220e-04
## HHAT       167.638967     -0.6021321 0.21091334 1.278244e-04 8.241060e-04
## FOXC1       23.672777      1.2884944 0.67317463 2.659619e-04 1.552415e-03
## F7          21.969485      1.5808522 0.53641763 1.344920e-05 1.123252e-04
## RASGRF1     94.140182      1.1681283 0.34399089 1.782696e-05 1.444325e-04
## PARP12      24.405251     -1.3648215 0.35994683 2.928443e-06 2.914986e-05
## YBX3      1001.227899     -0.6368817 0.12900294 2.130269e-08 3.486077e-07
## RIMBP2     473.676494      0.7814320 0.11799355 2.246110e-12 8.517523e-11
## MPC1       425.661915      0.7190435 0.21460239 2.356739e-05 1.859849e-04
## GUCY1B1    398.428899      1.0895907 0.15283239 1.525441e-13 6.829161e-12
## SEZ6       591.699557      0.9697650 0.17382167 2.530397e-09 5.283347e-08
## NGFR      1703.309930      1.3920001 0.17148193 2.372745e-17 1.795619e-15
## CNN2      1201.727345     -0.6939337 0.17762841 2.768533e-06 2.781373e-05
## ABCA7      347.950748      0.6183102 0.12087493 8.086490e-09 1.465888e-07
## HMG20B     779.189544     -1.0475951 0.16485359 2.865977e-11 9.014045e-10
## MCM10      400.286506     -1.1723274 0.28525996 1.797728e-06 1.890451e-05
## ANKRD44    460.609498      0.9252421 0.13225634 3.605022e-13 1.531251e-11
## TLE2        35.801382      0.6889568 0.43359801 3.434229e-03 1.380222e-02
## ME1          9.541013     -2.1157138 0.90317261 1.611341e-05 1.317195e-04
## NGEF        71.459698      1.4719380 0.27358914 1.796516e-09 3.891702e-08
## ASPM      1362.616996     -1.2601162 0.23219468 3.920750e-09 7.765325e-08
## FGFR2     1275.552836     -0.8622177 0.14696533 3.730293e-10 9.301222e-09
## KIF26A     285.174118      1.2377460 0.28510932 6.378378e-07 7.388856e-06
## PFKP      1032.139835     -0.6038054 0.15316524 2.158461e-06 2.229210e-05
## PHKA1      185.421052     -1.0406805 0.13589704 3.222728e-15 1.932522e-13
## PRKCZ      372.260418      0.9406259 0.17722155 9.985254e-09 1.770716e-07
## ATP2B3     174.188111      1.1967660 0.18754791 1.844796e-11 6.054983e-10
## ACSL4     1428.621028      0.7155171 0.05108957 7.952779e-46 4.752471e-43
## PRR11     1159.566332     -0.7313288 0.17902751 1.449642e-06 1.553636e-05
## REEP1     1338.125830      0.7652595 0.10584032 2.978449e-14 1.504855e-12
## RORA      1277.590519      0.8147867 0.17258425 1.169714e-07 1.603729e-06
## TGFBR3     108.485202     -0.6136344 0.41197675 5.281455e-03 1.975558e-02
## FGF10       28.238833     -1.0035408 0.95709257 1.527923e-03 6.900937e-03
## CHAT        23.974671      1.0684179 0.44400161 2.423508e-04 1.427095e-03
## TRIP13     237.668862     -1.0167318 0.20326750 4.954816e-08 7.408710e-07
## SPEG      1382.546481      0.7395804 0.12166303 5.487380e-11 1.633957e-09
## LNX1       111.678560      0.9637983 0.38031289 2.359393e-04 1.399325e-03
## HMMR       371.538865     -0.6390869 0.19108101 2.285548e-05 1.807784e-04
## TRNT1      314.267168     -0.7662216 0.14915573 1.260094e-08 2.170719e-07
## EVC        303.514220     -0.7450745 0.20430053 8.366581e-06 7.341410e-05
## NDE1       552.722825     -0.6743899 0.17548916 3.463455e-06 3.372005e-05
## IRAG1       95.810082     -0.9490872 0.19629746 1.001336e-07 1.397981e-06
## MCM2      1870.272466     -1.0232583 0.14972587 1.251388e-12 4.996903e-11
## ST6GAL1    379.864278      1.2892918 0.24686907 1.013559e-08 1.794175e-07
## GLI2      1511.655055     -0.6428594 0.08236856 1.633928e-16 1.146396e-14
## PPP2R2C    289.889331      1.2412984 0.21203318 3.913802e-10 9.648108e-09
## TEAD2     1219.154415     -0.6567162 0.13503388 3.257218e-08 5.067108e-07
## CA12       508.558506      1.1457841 0.21885865 1.451172e-08 2.455870e-07
## ENO1     10554.040630     -0.7655744 0.10582692 2.902145e-14 1.474903e-12
## SEMA3A     548.021439     -1.5219813 0.15819185 1.490321e-23 2.002114e-21
## GTSE1      486.670135     -1.1531416 0.16718324 6.796513e-13 2.817789e-11
## ZNF37A     110.743181      4.2026150 0.34319091 7.457127e-36 2.485231e-33
## CACNG5     225.061635      0.7734686 0.27311184 1.293530e-04 8.324127e-04
## WDR62      333.109321     -0.9017119 0.15439254 5.031529e-10 1.212746e-08
## ARHGAP15    22.274407      0.9105352 0.44408139 7.512258e-04 3.787087e-03
## PAX2       324.551902      1.4902226 0.47508362 1.179454e-05 1.000976e-04
## RGS11      120.008733     -1.1194503 0.32041405 1.490395e-05 1.231691e-04
## SPAG5      898.227860     -0.6350088 0.12784573 1.817515e-08 3.022796e-07
## TPD52      307.232828     -1.4609820 0.17557562 2.887332e-18 2.338199e-16
## ACACB      238.611693     -0.7001358 0.18261454 3.752997e-06 3.609292e-05
## MBNL3      331.883748     -0.7653085 0.18396819 1.164398e-06 1.276345e-05
## SLC25A43    46.151083     -0.9808211 0.30692688 4.210240e-05 3.106150e-04
## NEBL       525.999884      0.7176653 0.14492411 2.594948e-08 4.140925e-07
## ADCY2      433.464629      0.8206519 0.19782965 1.417476e-06 1.522930e-05
## RBFOX1      50.519246      4.2956286 0.67134124 3.225621e-12 1.191898e-10
## OPHN1      718.035736      0.8767450 0.09062942 6.200465e-23 8.202600e-21
## EPB41L2    901.360735     -0.8968172 0.13108224 9.474693e-13 3.845350e-11
## SLC4A4     182.442551      1.4163259 0.17253701 9.696656e-18 7.569507e-16
## SESN1      883.220023     -0.8258933 0.08573464 6.972073e-23 9.084664e-21
## NDC80      394.130899     -1.0195247 0.23237775 7.295614e-07 8.323435e-06
## TCF7       111.696159     -1.5635780 0.29654406 1.819091e-09 3.925883e-08
## ARG2       345.081013      0.6256698 0.13064076 4.406662e-08 6.646428e-07
## STK17B     177.081242     -0.8554177 0.21759756 3.552769e-06 3.448852e-05
## ZNF506     962.327475      0.6208659 0.11363297 1.199390e-09 2.688930e-08
## PCDHA6     296.195905      3.1209433 0.31997928 4.736670e-25 7.015939e-23
## PGR         24.032531     -0.9350518 0.85663109 1.912697e-03 8.364128e-03
## SERTAD4    795.485996      1.4532558 0.16116771 6.861592e-21 7.721519e-19
## TRAF5      101.415939     -1.1842021 0.34680897 1.626345e-05 1.327582e-04
## LYRM2     1028.536379     -0.8809687 0.07483407 9.925374e-33 2.606163e-30
## PLOD1      242.133783     -0.6875288 0.31529300 8.629754e-04 4.254726e-03
## ZNF671     140.840542     -1.1010592 0.21290580 2.128301e-08 3.486077e-07
## SLCO1A2    139.594979      3.1285375 0.31103471 2.412175e-26 3.800273e-24
## EFR3B     1751.877875      0.5903274 0.18872692 5.102135e-05 3.682633e-04
## KIF3C     4319.863302      0.6023546 0.06947780 1.002189e-19 1.027689e-17
## MECOM       89.985242      3.6050725 0.40896597 1.582692e-20 1.735953e-18
## OVGP1      136.008284      0.9456670 0.15573359 1.467956e-10 4.010581e-09
## ORC1       210.576080     -1.1833541 0.22265559 8.929921e-09 1.605348e-07
## RAD54L     234.230732     -1.2337034 0.21035925 3.783097e-10 9.365867e-09
## MAST2     3220.188799      0.7029323 0.10129350 1.521944e-13 6.829161e-12
## EPDR1      241.452195      0.9000096 0.15627529 7.931098e-10 1.844912e-08
## HBQ1         6.559051     -0.9851499 0.80377562 1.520114e-03 6.872836e-03
## PPEF1       57.691395      0.8091799 0.34782309 4.996582e-04 2.674206e-03
## TRIP6      275.792394     -1.1209387 0.17854886 4.265707e-11 1.299204e-09
## BAX        799.257173     -0.7162476 0.06843482 6.279169e-27 1.066843e-24
## ADAMTS2    135.102911      1.3855640 0.42866141 1.383202e-05 1.151893e-04
## MT3         79.628533      0.7051887 0.49305587 4.251150e-03 1.646274e-02
## GNAO1     4552.249667      0.5927987 0.05740865 1.189671e-26 1.926822e-24
## AURKA      300.278380     -0.9914771 0.22506292 6.713440e-07 7.738474e-06
## GP6         22.577373      0.6142667 0.34124814 2.627868e-03 1.098895e-02
## TPX2      1709.906575     -1.0349423 0.16511888 4.935188e-11 1.479702e-09
## SLC4A11     29.522371     -1.4208622 0.41166451 6.621182e-06 5.957689e-05
## CPXM1     1732.311448     -0.9311296 0.08372028 2.027233e-29 4.504095e-27
## TESC        38.528571     -0.8706273 0.33769762 2.449484e-04 1.440433e-03
## BIRC5      867.249319     -1.1606635 0.23089062 3.914320e-08 5.966154e-07
## IRAK3       34.463668     -0.7316807 0.28647724 2.949696e-04 1.705078e-03
## KIF4A      730.454231     -1.0681275 0.23605548 4.122533e-07 4.985589e-06
## PUS7       248.025204     -0.6865120 0.15679592 3.595553e-07 4.434941e-06
## LAMB1      414.330555      0.6843124 0.58031455 5.930887e-03 2.174072e-02
## ABCC6        7.352935     -0.5991774 0.55461332 9.527558e-03 3.224855e-02
## NLRP1       13.796473      0.7291549 0.53659557 4.219445e-03 1.638352e-02
## ZFHX4     2940.527602     -1.0053600 0.17435033 9.402161e-10 2.149597e-08
## RGS17      575.541394      0.5938164 0.09093100 1.567694e-12 6.132763e-11
## MYH7       148.921807      1.4693108 0.33617218 2.186238e-07 2.833769e-06
## SEMA6A    2382.053881      0.7387983 0.13034934 6.195240e-10 1.478836e-08
## WDR76      170.177471     -1.9418282 0.23753813 3.106147e-19 2.957666e-17
## COL9A3      53.562081      0.9695474 0.48890090 7.158719e-04 3.630688e-03
## CLSPN      398.813772     -0.7428961 0.22160887 2.400967e-05 1.890448e-04
## CDC45      183.122205     -1.1630991 0.29699942 3.609933e-06 3.498460e-05
## COMT       334.310116     -6.2678284 0.34471921 9.823899e-75 1.891646e-71
## ADA2       157.297438     -0.7408660 0.22566980 3.040100e-05 2.325019e-04
## XYLB        50.307399     -1.0409517 0.29834040 1.689706e-05 1.375416e-04
## CDC6       264.023284     -1.0963213 0.28045003 4.127490e-06 3.921568e-05
## EPB41L4B   226.844879      0.7559146 0.15030206 2.078035e-08 3.419376e-07
## CYP26A1    420.931158     -1.3529330 0.70074047 2.106317e-04 1.269210e-03
## CRTAC1     115.948218      0.6718855 0.34076237 1.516901e-03 6.860098e-03
## FKBP5      652.044694     -0.9495623 0.08646333 9.841034e-29 2.079819e-26
## PCDH11Y     28.507227      0.7360721 0.45255290 2.766723e-03 1.147065e-02
## HNRNPM    4415.756986     -0.6089637 0.09319301 1.563863e-12 6.132763e-11
## SLC7A4      11.454227     -4.6046071 0.88946172 3.161345e-09 6.392779e-08
## SEZ6L     2049.299359      0.9889352 0.29399746 2.567680e-05 2.000804e-04
## LGALS1      71.686130      1.2568887 0.49244825 1.011132e-04 6.698365e-04
## SOX10       12.272518      0.8163050 1.18557450 2.940419e-03 1.206733e-02
## CENPM      118.687481     -0.7672282 0.21567317 1.202597e-05 1.017130e-04
## SEPTIN3  12294.134164      0.6614896 0.08131416 1.261031e-17 9.756102e-16
## SLC5A4       4.345687      0.7348124 0.91266436 4.032553e-03 1.581447e-02
## TIMP3      275.667631      1.0044593 0.42216763 3.033876e-04 1.743850e-03
## MCM5       955.075706     -0.8794455 0.17585069 3.888773e-08 5.932434e-07
## TSPO        49.359249     -1.2938861 0.32372038 1.908296e-06 1.994618e-05
## RASD2       78.213329      0.6901931 0.46245857 4.073060e-03 1.593366e-02
## APOL4       20.507939      1.5797718 0.59197682 2.598091e-05 2.017677e-04
## PNPLA3     322.158923      0.9305688 0.08838558 1.279315e-26 2.052827e-24
##  [ reached 'max' / getOption("max.print") -- omitted 1544 rows ]
DEAList_day50_AR
## $dds
## class: DESeqDataSet 
## dim: 17673 14 
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17673): TSPAN6 TNMD ... NPBWR1 PDCD6-AHRR
## rowData names(47): Gene EnsGene ... deviance maxCooks
## colnames(14): OLE_010 OLE_011 ... OLE_048 OLE_049
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
## 
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 17673 rows and 6 columns
##                baseMean log2FoldChange     lfcSE       stat    pvalue      padj
##               <numeric>      <numeric> <numeric>  <numeric> <numeric> <numeric>
## TSPAN6       1022.69733       0.244252 0.1192471   2.048285 0.0405320 0.1526386
## TNMD            7.74747       0.671671 1.1834179   0.567569 0.5703278        NA
## DPM1          566.77011       0.181490 0.0999239   1.816287 0.0693263 0.2169459
## SCYL3         326.10166      -0.077452 0.1058136  -0.731967 0.4641889 0.6804306
## C1orf112      220.67316       0.333052 0.1356996   2.454331 0.0141147 0.0735165
## ...                 ...            ...       ...        ...       ...       ...
## LINC01949       6.08511      -0.435760  0.705506 -0.6176550  0.536803        NA
## C8orf44       175.25242       0.217527  0.189150  1.1500194  0.250136  0.479973
## C8orf44-SGK3   11.64862      -0.676492  0.684428 -0.9884044  0.322955        NA
## NPBWR1          3.66410      -0.603128  1.068740 -0.5643352  0.572526        NA
## PDCD6-AHRR     40.02742       0.259541  2.661601  0.0975133  0.922319  0.962337
## 
## $AR$DEGs
##            baseMean log2FoldChange      lfcSE       stat       pvalue         padj
## HECW1     487.01206     -0.6907292 0.15649437  -4.413764 1.015888e-05 3.214922e-04
## CYP26B1  2066.77989     -1.7743093 0.39521143  -4.489519 7.138414e-06 2.456187e-04
## SLC7A2     71.45486      0.8495051 0.21178343   4.011197 6.041161e-05 1.315440e-03
## PRKAR2B  2149.63295     -0.6062280 0.10519453  -5.762923 8.266931e-09 8.676709e-07
## ITGA3     260.50731     -0.7856492 0.18879742  -4.161334 3.163933e-05 7.890018e-04
## TAC1      182.89786     -1.2284544 0.33653780  -3.650272 2.619630e-04 4.048494e-03
## MAP3K9   1045.22555     -0.5908176 0.09412563  -6.276905 3.453788e-10 5.927920e-08
## SYN1      721.45461     -0.6133381 0.12050585  -5.089696 3.586379e-07 2.051831e-05
## TFAP2B   5409.28759     -0.6033988 0.22197892  -2.718271 6.562415e-03 4.287464e-02
## MGST1     437.04491      0.7509057 0.16476438   4.557452 5.177790e-06 1.897959e-04
## ST3GAL1   135.72797     -0.7938796 0.17708847  -4.482955 7.361645e-06 2.527036e-04
## GABRA3    551.70082     -0.6320979 0.21014021  -3.007982 2.629889e-03 2.244570e-02
## SLC7A14   261.11613     -0.7694304 0.18421051  -4.176908 2.954984e-05 7.484420e-04
## MAMLD1    291.21047     -0.6021508 0.14274938  -4.218237 2.462194e-05 6.507419e-04
## POLA2     314.19462      0.6243013 0.15170496   4.115233 3.867884e-05 9.301450e-04
## CNTN1    1292.52799     -0.8980093 0.18133330  -4.952258 7.335713e-07 3.822168e-05
## SYT13    1975.68793     -0.6820510 0.15259826  -4.469585 7.837133e-06 2.658975e-04
## CPS1      590.87086      0.7858847 0.26918313   2.919517 3.505743e-03 2.758645e-02
## TNFRSF1B   20.53158      1.3483326 0.49969137   2.698331 6.968817e-03 4.468927e-02
## LRRC7     771.70960     -0.7323077 0.18193853  -4.025028 5.696851e-05 1.261174e-03
## FLT4      137.23741      0.5858991 0.20703866   2.829902 4.656229e-03 3.357871e-02
## PTPRN     430.82937     -0.6589206 0.14964135  -4.403332 1.066008e-05 3.344513e-04
## CAMK2B    626.02245     -0.7008505 0.19618301  -3.572432 3.536807e-04 5.134177e-03
## RIMBP2    473.67649     -0.7310915 0.12911898  -5.662153 1.494853e-08 1.425386e-06
## GUCY1B1   398.42890     -0.5971475 0.17760624  -3.362199 7.732440e-04 9.231471e-03
## SEZ6      591.69956     -1.0928209 0.19510850  -5.601093 2.130043e-08 1.930137e-06
## DGKA      131.46923     -0.6339446 0.20161166  -3.144385 1.664365e-03 1.601677e-02
## ANKRD44   460.60950     -0.6781740 0.14879171  -4.557875 5.167383e-06 1.897959e-04
## MPPED2    195.15180     -1.0001391 0.30323302  -3.298252 9.728862e-04 1.091803e-02
## FGFR2    1275.55284      0.8701210 0.15596172   5.579068 2.418108e-08 2.151084e-06
## PRKCZ     372.26042     -0.6296375 0.19742566  -3.189238 1.426483e-03 1.428343e-02
## NAV3      705.74594     -0.9376056 0.15338510  -6.112755 9.792536e-10 1.414488e-07
## ATP2B3    174.18811     -0.7659533 0.22044869  -3.474520 5.117687e-04 6.720246e-03
## REEP1    1338.12583     -0.6745331 0.11535704  -5.847351 4.994627e-09 5.614326e-07
## RORA     1277.59052     -0.6784940 0.18510667  -3.665422 2.469315e-04 3.903016e-03
## SPTB       51.02704     -1.5217026 0.49162931  -3.095224 1.966646e-03 1.807902e-02
## JMJD6     709.60535     -0.6042578 0.10151187  -5.952583 2.639437e-09 3.291175e-07
## WIPI1     273.05663     -0.5901246 0.16842401  -3.503803 4.586639e-04 6.230398e-03
## LNX1      111.67856     -1.3153893 0.41472685  -3.171700 1.515493e-03 1.494897e-02
## TRNT1     314.26717      0.6254685 0.15333473   4.079105 4.520940e-05 1.051954e-03
## PPP2R2C   289.88933     -0.9463518 0.24261314  -3.900662 9.593016e-05 1.890797e-03
## FOSL2     149.84291     -0.9459509 0.28439173  -3.326225 8.803079e-04 1.009655e-02
## ACTL6B    584.34135     -0.5881736 0.15456370  -3.805380 1.415867e-04 2.559613e-03
## RUNX1T1  2142.26638     -0.7259861 0.14760562  -4.918418 8.724667e-07 4.404297e-05
## MID2       74.23563     -0.7168293 0.21487353  -3.336052 8.497725e-04 9.857507e-03
## ZNF506    962.32747     -1.2589937 0.12422565 -10.134733 3.874317e-24 9.420403e-21
## PCDHA6    296.19590     -1.4038942 0.37162810  -3.777686 1.582924e-04 2.776401e-03
## SERTAD4   795.48600     -1.1602950 0.18501410  -6.271387 3.578465e-10 6.070491e-08
## ZNF671    140.84054     -1.3109240 0.24191472  -5.418951 5.994981e-08 4.508288e-06
## SLCO1A2   139.59498      1.0204619 0.34723595   2.938814 3.294706e-03 2.635223e-02
## B4GALT1   105.08576      1.0061745 0.32751762   3.072123 2.125420e-03 1.914059e-02
## TRIP6     275.79239      0.6302696 0.19403048   3.248302 1.160960e-03 1.230904e-02
## PPP1R13B  302.63845     -0.6434349 0.17285260  -3.722449 1.973000e-04 3.312325e-03
## LHX5     1171.05998     -0.7357898 0.24907485  -2.954091 3.135916e-03 2.555859e-02
## PUS7      248.02520      0.5957092 0.15108028   3.942998 8.046941e-05 1.653476e-03
## ITGA6     659.49194      0.6335637 0.19973883   3.171961 1.514136e-03 1.494569e-02
## RAPGEF4   203.96388     -0.7466078 0.26071889  -2.863651 4.187898e-03 3.129982e-02
## MYO15A    173.82548     -0.7563342 0.26970261  -2.804327 5.042179e-03 3.567427e-02
## HAUS4     282.74382      0.6000578 0.12675042   4.734168 2.199552e-06 9.607563e-05
## MYH7      148.92181     -1.5324051 0.39006220  -3.928617 8.543565e-05 1.735962e-03
## TBC1D2    100.36716     -0.9549873 0.20160530  -4.736915 2.169956e-06 9.506755e-05
## SORBS1   1870.38956     -0.8139636 0.11202627  -7.265828 3.707611e-13 1.590892e-10
## FKBP5     652.04469      0.6067950 0.09035786   6.715465 1.874677e-11 4.635535e-09
## SYDE2      74.81199      0.7509018 0.25763322   2.914616 3.561269e-03 2.797811e-02
## GCAT      184.02729      0.6814468 0.15931227   4.277428 1.890648e-05 5.336350e-04
## HMOX1     109.61352     -0.9664701 0.33468844  -2.887671 3.881057e-03 2.967544e-02
## CACNA1I   139.64094     -0.6910552 0.21947057  -3.148738 1.639774e-03 1.583234e-02
## MLC1      333.92944     -1.0562664 0.36730063  -2.875754 4.030632e-03 3.056283e-02
## SLC8A3    173.22246     -0.5883779 0.21684964  -2.713299 6.661702e-03 4.334793e-02
## GINS1     572.76183      0.6298919 0.13355635   4.716301 2.401714e-06 1.041116e-04
## SALL4     979.82904      0.8420850 0.17988104   4.681344 2.850006e-06 1.177868e-04
## EEF1A2   2804.26303     -0.8454354 0.16411694  -5.151420 2.585208e-07 1.558496e-05
## RSPO4      17.10572     -1.7747848 0.60488034  -2.934109 3.345069e-03 2.665276e-02
## PAK5      688.93372     -0.6078029 0.11893983  -5.110171 3.218675e-07 1.893437e-05
## PXMP4      55.47597     -0.8919618 0.28885404  -3.087933 2.015542e-03 1.842402e-02
## SLC32A1   159.37572     -1.0480505 0.39106540  -2.679988 7.362487e-03 4.647829e-02
## MAP1LC3A  316.96118     -0.7841432 0.21015916  -3.731187 1.905796e-04 3.221251e-03
## SYNDIG1    73.38811     -1.5612687 0.37857761  -4.124039 3.722863e-05 9.048500e-04
## CELF4    1137.94217     -1.0377688 0.18142766  -5.720014 1.065151e-08 1.042918e-06
## LAMA1    1523.04638      0.6854075 0.18509644   3.702975 2.130860e-04 3.489014e-03
## NOL4      270.45722     -0.8733645 0.17997077  -4.852813 1.217226e-06 5.860760e-05
## GLRA2     368.11726     -0.5964749 0.19137762  -3.116743 1.828606e-03 1.717807e-02
## PCSK1N   1068.34148     -0.7938771 0.13883006  -5.718337 1.075714e-08 1.046239e-06
## PCYT1B    578.97050     -0.8526841 0.29425309  -2.897792 3.758001e-03 2.902355e-02
## NALCN     160.49898     -0.9790393 0.26363728  -3.713584 2.043443e-04 3.383858e-03
## FGF14     320.14051     -0.7650080 0.20973199  -3.647551 2.647523e-04 4.082950e-03
## HSF4      256.97648     -0.9801072 0.21595324  -4.538516 5.665151e-06 2.055942e-04
## CBLN1     658.76042     -1.1952750 0.28825606  -4.146574 3.374877e-05 8.316906e-04
## NDRG4    5440.45822     -0.6614156 0.09254452  -7.146999 8.869584e-13 3.405220e-10
## SMPD3     831.99622     -0.7035602 0.16113199  -4.366359 1.263346e-05 3.839783e-04
## COTL1    2455.05714      0.6383814 0.22782189   2.802107 5.076997e-03 3.574725e-02
## NDRG1     369.35800     -0.7079784 0.12098240  -5.851912 4.859537e-09 5.538733e-07
## TUBB4A    817.07522     -0.6112838 0.16602248  -3.681934 2.314711e-04 3.710915e-03
## OLFM2     888.35290     -0.6002730 0.10736759  -5.590821 2.259990e-08 2.022760e-06
## ICAM5     372.27628     -0.8596440 0.30318919  -2.835339 4.577715e-03 3.322601e-02
## PLA2G4C   164.03506     -0.8797805 0.27116419  -3.244457 1.176748e-03 1.242302e-02
## PLEKHA4    88.49805      0.6288101 0.22709752   2.768899 5.624609e-03 3.820691e-02
## LSR        69.82980      1.1389656 0.41318387   2.756559 5.841314e-03 3.930869e-02
## ADAP1     277.83758     -0.6935407 0.16197118  -4.281877 1.853232e-05 5.280626e-04
## CHN2      512.35806     -0.5907985 0.18039336  -3.275057 1.056408e-03 1.151864e-02
## TFR2      141.02274     -0.6428842 0.18970638  -3.388838 7.018946e-04 8.568988e-03
## RARRES2   250.59407      1.0333329 0.31438458   3.286843 1.013172e-03 1.117246e-02
## SLC1A1    182.38777     -0.9388668 0.22226444  -4.224098 2.398993e-05 6.398337e-04
## APBA1    1178.47207     -0.6075032 0.09492808  -6.399616 1.557686e-10 2.951309e-08
## UNC5B     745.09403     -0.6358846 0.23677464  -2.685611 7.239732e-03 4.590197e-02
## ACTA2     237.53091      0.5877620 0.19212238   3.059310 2.218473e-03 1.972291e-02
## CPEB3     387.33347     -0.6045211 0.14920835  -4.051524 5.088518e-05 1.156330e-03
## NEURL1    195.67888     -0.6716159 0.20053500  -3.349120 8.106856e-04 9.545676e-03
## EBF3     4287.46260     -0.8817441 0.30468928  -2.893912 3.804742e-03 2.930696e-02
## SLC9A3R1  347.95319      0.6059950 0.11965928   5.064337 4.098232e-07 2.326425e-05
## NEIL3      89.90259      0.6299136 0.23417141   2.689968 7.145889e-03 4.544765e-02
## CRYAB     191.95576     -1.0193845 0.37261733  -2.735741 6.223998e-03 4.116134e-02
## ZBTB16   1475.08472      0.7293083 0.16102729   4.529097 5.923618e-06 2.123333e-04
## JHY       123.49121     -0.6145456 0.17082125  -3.597594 3.211740e-04 4.752137e-03
## TMEM109   150.62458      0.7540878 0.24986145   3.018024 2.544288e-03 2.180882e-02
## MDK      4935.19503      0.6000171 0.18095701   3.315799 9.138147e-04 1.038290e-02
## PTPN5     633.09891     -0.7079480 0.19528763  -3.625155 2.887878e-04 4.383747e-03
## FZD10     575.91129     -4.4934503 0.89616574  -5.014084 5.328670e-07 2.868633e-05
## TIMELESS 1544.91963      0.6101987 0.07638003   7.988982 1.360576e-15 1.167614e-12
## PRDM13    478.64470     -3.0886164 1.10863311  -2.785968 5.336813e-03 3.693490e-02
## GMNN      399.54015      0.6030139 0.14257937   4.229321 2.343979e-05 6.274551e-04
## ARFGEF3   743.06469     -0.7104958 0.15191243  -4.677009 2.910901e-06 1.196257e-04
## VEGFA    3223.50057     -0.5933773 0.13631652  -4.352937 1.343255e-05 4.023973e-04
## LAMA4     227.72897     -1.1394380 0.26700242  -4.267519 1.976586e-05 5.503133e-04
## SEMA5A    452.89603     -0.7963641 0.26979412  -2.951747 3.159814e-03 2.569595e-02
## HBEGF     117.97187     -0.8550975 0.20143364  -4.245058 2.185369e-05 5.926086e-04
## LOX        52.91890     -0.9307586 0.34764299  -2.677340 7.420925e-03 4.680669e-02
## CDH9       71.05775     -1.4707326 0.30217618  -4.867136 1.132271e-06 5.524652e-05
## GABRG2    250.76094     -0.7653228 0.19583931  -3.907912 9.309724e-05 1.847885e-03
## IRX4      109.14909     -1.1547042 0.37554308  -3.074758 2.106732e-03 1.904282e-02
## PDE4D     644.61321     -0.7640558 0.14976739  -5.101617 3.367640e-07 1.957390e-05
## FGF1       61.26147     -2.1461114 0.50910241  -4.215481 2.492467e-05 6.562314e-04
## STC2      377.19120     -1.0170877 0.20226161  -5.028575 4.941382e-07 2.699994e-05
## RBP1       78.17264      0.7070523 0.22585640   3.130539 1.744858e-03 1.661030e-02
## HES1      193.37661      0.6500032 0.21633440   3.004622 2.659107e-03 2.256697e-02
## CBLB     3110.26108     -0.6175992 0.14049973  -4.395732 1.103999e-05 3.434168e-04
## SLC4A3    453.10081     -0.7103553 0.20234735  -3.510574 4.471409e-04 6.113719e-03
## FNDC4     357.63594     -0.6405876 0.11772042  -5.441601 5.280379e-08 4.075950e-06
## REEP6     166.66410      0.6120657 0.19675477   3.110805 1.865782e-03 1.744865e-02
## EFHD1      45.27727      1.0971606 0.40501176   2.708960 6.749449e-03 4.376343e-02
## ABCB6     356.18783     -0.8998530 0.24444336  -3.681233 2.321084e-04 3.713824e-03
## SLC5A7     84.10572     -1.3582683 0.40332656  -3.367664 7.580793e-04 9.074020e-03
## CHD5      880.41216     -1.3151600 0.19128616  -6.875353 6.183639e-12 1.640238e-09
## DNAJC6   1202.22654     -0.5991277 0.12356222  -4.848794 1.242145e-06 5.961070e-05
## PADI2      74.93590     -1.0878750 0.27551545  -3.948508 7.863970e-05 1.625035e-03
## ID3       300.37043      0.9848902 0.35857870   2.746650 6.020733e-03 4.033429e-02
## PLPPR4    144.22961     -0.9718173 0.19916815  -4.879381 1.064193e-06 5.245103e-05
## RCAN3     233.93395     -0.8551895 0.20102898  -4.254061 2.099283e-05 5.764108e-04
## SLC8A2    471.20168     -1.0713419 0.15553857  -6.887950 5.660194e-12 1.529196e-09
## TTR      1756.71399      5.6839770 1.65676324   3.430772 6.018662e-04 7.661978e-03
## CA14      867.00386      0.6588013 0.16292095   4.043687 5.261722e-05 1.190128e-03
## ATP10B     23.79733     -2.6889323 0.97334113  -2.762580 5.734658e-03 3.873284e-02
## SGIP1    1031.61306     -0.6744190 0.11418647  -5.906295 3.498868e-09 4.253749e-07
## PLAGL1   1832.94449      0.7622864 0.18147199   4.200573 2.662402e-05 6.913515e-04
## STBD1      18.53196     -2.0402858 0.67999636  -3.000436 2.695931e-03 2.274890e-02
## NEK6      513.50080      0.6865989 0.19449893   3.530091 4.154169e-04 5.777423e-03
## ACOT2      26.63873     -1.5925513 0.49438887  -3.221252 1.276317e-03 1.314816e-02
## BCL11A   1120.51422     -1.0980020 0.37709399  -2.911746 3.594146e-03 2.816058e-02
## PPP1R3C   202.27271     -1.1546142 0.28552456  -4.043835 5.258395e-05 1.190128e-03
## MSX2      141.71316      0.6903719 0.22636253   3.049851 2.289553e-03 2.019485e-02
## MOB3B     305.75607      0.8888636 0.23948645   3.711540 2.060019e-04 3.406372e-03
## GRIA2    3436.40870     -0.8062087 0.10123242  -7.963938 1.666486e-15 1.350687e-12
## IQSEC3    263.74290     -0.7711870 0.19019957  -4.054620 5.021588e-05 1.143495e-03
## ENOX1     301.86054     -0.5899052 0.18920155  -3.117867 1.821652e-03 1.713481e-02
## DNAJC15    58.88974     -1.3174093 0.41719704  -3.157763 1.589849e-03 1.548352e-02
## MND1      128.94045      0.6792427 0.24825036   2.736120 6.216838e-03 4.116134e-02
##  [ reached 'max' / getOption("max.print") -- omitted 486 rows ]
## 
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT 
## Wald test p-value: Genotype AR vs WT 
## DataFrame with 17673 rows and 5 columns
##                baseMean log2FoldChange     lfcSE    pvalue      padj
##               <numeric>      <numeric> <numeric> <numeric> <numeric>
## TSPAN6       1022.69733      0.1522423 0.1045269 0.0405320 0.1526386
## TNMD            7.74747      0.0200873 0.2068027 0.5703278        NA
## DPM1          566.77011      0.1213324 0.0877772 0.0693263 0.2169459
## SCYL3         326.10166     -0.0463086 0.0833705 0.4641889 0.6804306
## C1orf112      220.67316      0.2043966 0.1244734 0.0141147 0.0735165
## ...                 ...            ...       ...       ...       ...
## LINC01949       6.08511    -0.03111170  0.192102  0.536803        NA
## C8orf44       175.25242     0.08654881  0.127079  0.250136  0.479973
## C8orf44-SGK3   11.64862    -0.05226779  0.199953  0.322955        NA
## NPBWR1          3.66410    -0.02154627  0.204268  0.572526        NA
## PDCD6-AHRR     40.02742     0.00179369  0.221336  0.922319  0.962337
## 
## $AR$DEGsAshr
##               baseMean log2FoldChange      lfcSE       pvalue         padj
## CYP26B1     2066.77989     -1.0835803 0.46939809 7.138414e-06 2.456187e-04
## SLC7A2        71.45486      0.6023608 0.23960462 6.041161e-05 1.315440e-03
## ITGA3        260.50731     -0.5867822 0.21136483 3.163933e-05 7.890018e-04
## TAC1         182.89786     -0.6306273 0.37608400 2.619630e-04 4.048494e-03
## MGST1        437.04491      0.6030447 0.18088326 5.177790e-06 1.897959e-04
## ST3GAL1      135.72797     -0.6267032 0.19570080 7.361645e-06 2.527036e-04
## CNTN1       1292.52799     -0.7413694 0.19542325 7.335713e-07 3.822168e-05
## RIMBP2       473.67649     -0.6462762 0.13645402 1.494853e-08 1.425386e-06
## SEZ6         591.69956     -0.9281845 0.19947034 2.130043e-08 1.930137e-06
## FGFR2       1275.55284      0.7584071 0.16420290 2.418108e-08 2.151084e-06
## NAV3         705.74594     -0.8356237 0.15787126 9.792536e-10 1.414488e-07
## REEP1       1338.12583     -0.6033967 0.12107832 4.994627e-09 5.614326e-07
## PPP2R2C      289.88933     -0.6284082 0.27646206 9.593016e-05 1.890797e-03
## RUNX1T1     2142.26638     -0.6089667 0.15941071 8.724667e-07 4.404297e-05
## ZNF506       962.32747     -1.1912259 0.12333412 3.874317e-24 9.420403e-21
## PCDHA6       296.19590     -0.6994985 0.41792184 1.582924e-04 2.776401e-03
## SERTAD4      795.48600     -1.0145416 0.18475458 3.578465e-10 6.070491e-08
## ZNF671       140.84054     -1.0568784 0.24584686 5.994981e-08 4.508288e-06
## MYH7         148.92181     -0.7791067 0.44571466 8.543565e-05 1.735962e-03
## TBC1D2       100.36716     -0.7613363 0.21918921 2.169956e-06 9.506755e-05
## SORBS1      1870.38956     -0.7582790 0.11514212 3.707611e-13 1.590892e-10
## SALL4        979.82904      0.6785370 0.19709059 2.850006e-06 1.177868e-04
## EEF1A2      2804.26303     -0.7158294 0.17582676 2.585208e-07 1.558496e-05
## SYNDIG1       73.38811     -0.8721943 0.43678181 3.722863e-05 9.048500e-04
## CELF4       1137.94217     -0.8954958 0.18602107 1.065151e-08 1.042918e-06
## NOL4         270.45722     -0.7155261 0.19525590 1.217226e-06 5.860760e-05
## PCSK1N      1068.34148     -0.7014512 0.14643851 1.075714e-08 1.046239e-06
## NALCN        160.49898     -0.5969406 0.29951384 2.043443e-04 3.383858e-03
## HSF4         256.97648     -0.7541013 0.23776619 5.665151e-06 2.055942e-04
## CBLN1        658.76042     -0.7848100 0.32588859 3.374877e-05 8.316906e-04
## NDRG4       5440.45822     -0.6166119 0.09547001 8.869584e-13 3.405220e-10
## NDRG1        369.35800     -0.6324720 0.12723716 4.859537e-09 5.538733e-07
## SLC1A1       182.38777     -0.6846382 0.25019870 2.398993e-05 6.398337e-04
## ZBTB16      1475.08472      0.5853223 0.17660000 5.923618e-06 2.123333e-04
## FZD10        575.91129     -4.0299392 1.21947054 5.328670e-07 2.868633e-05
## LAMA4        227.72897     -0.7916409 0.29911133 1.976586e-05 5.503133e-04
## HBEGF        117.97187     -0.6395226 0.22596112 2.185369e-05 5.926086e-04
## CDH9          71.05775     -1.0672426 0.32234353 1.132271e-06 5.524652e-05
## PDE4D        644.61321     -0.6491157 0.16098947 3.367640e-07 1.957390e-05
## FGF1          61.26147     -1.0319144 0.68147757 2.492467e-05 6.562314e-04
## STC2         377.19120     -0.8314402 0.21459402 4.941382e-07 2.699994e-05
## CHD5         880.41216     -1.1571236 0.18972621 6.183639e-12 1.640238e-09
## PADI2         74.93590     -0.6944796 0.31423763 7.863970e-05 1.625035e-03
## PLPPR4       144.22961     -0.7868665 0.21425458 1.064193e-06 5.245103e-05
## RCAN3        233.93395     -0.6407654 0.22540970 2.099283e-05 5.764108e-04
## SLC8A2       471.20168     -0.9697724 0.15542084 5.660194e-12 1.529196e-09
## SGIP1       1031.61306     -0.6048738 0.11972067 3.498868e-09 4.253749e-07
## PPP1R3C      202.27271     -0.7429776 0.32463159 5.258395e-05 1.190128e-03
## GRIA2       3436.40870     -0.7612220 0.10351358 1.666486e-15 1.350687e-12
## CSMD2        968.85062     -0.9975840 0.21860932 2.716644e-08 2.373240e-06
## SV2C         181.54089     -0.6870908 0.33478466 1.093457e-04 2.101771e-03
## MYOG          18.32726    -28.4438965 2.73349284 9.108461e-26 2.657667e-22
## OPTN        1270.74730     -0.5907463 0.12929978 3.893876e-08 3.209478e-06
## GRM4          98.25386     -0.6056921 0.24289994 6.270242e-05 1.351205e-03
## MYRF         165.04781      0.6124310 0.26124331 8.791176e-05 1.776378e-03
## BCL11B       272.25764     -0.7782329 0.34983758 4.883559e-05 1.123758e-03
## TUBA4A        47.10089     -0.8856634 0.37207517 2.054090e-05 5.695814e-04
## FOXP2       2111.20008     -1.2294256 0.34846278 2.221390e-07 1.361675e-05
## SH3BP5      1119.36393     -0.7261173 0.11382197 1.333594e-12 4.745318e-10
## LIN28A       354.56596      1.1826473 0.33542393 3.122305e-07 1.844182e-05
## TRIM22       366.51838     -0.5970849 0.13113192 4.083604e-08 3.322214e-06
## SNAP25      1313.11192     -0.5996452 0.13292011 4.904921e-08 3.867994e-06
## ATP8A2       520.75282     -0.6712739 0.26497561 4.259893e-05 1.007254e-03
## GPR12         95.93084     -0.9025200 0.38937905 2.049893e-05 5.695814e-04
## MYH8          44.93433    -28.5494118 4.00270460 3.706420e-13 1.590892e-10
## MYBPH         26.81626    -28.5073035 4.04663738 7.001476e-13 2.760663e-10
## SPINK5       266.61273      1.2096813 0.36170530 4.165138e-07 2.355240e-05
## DUSP26       387.34465     -0.8545376 0.20669771 1.848690e-07 1.162523e-05
## CTIF        3452.04548     -0.5859326 0.06794082 6.605973e-20 9.637454e-17
## BHLHE40      165.75434     -0.9007862 0.28238838 3.425414e-06 1.365392e-04
## TFCP2        940.41623     -0.8827923 0.12649201 4.046111e-14 2.186248e-11
## FAIM2        916.62971     -0.6180551 0.18952595 6.259477e-06 2.211126e-04
## RAPGEF5      578.40470     -0.8124025 0.17901628 3.552327e-08 2.961423e-06
## RALGPS1     1967.56501     -0.5986361 0.08385303 8.719221e-15 5.530640e-12
## PAK6         206.47580     -0.6901740 0.16225023 1.246026e-07 8.225466e-06
## STRA6        231.73094      0.7466667 0.27134291 1.837965e-05 5.251948e-04
## PCDH10       798.86844     -1.5259672 0.28415445 5.095997e-12 1.457755e-09
## RASGEF1B     345.78989     -0.8616650 0.22085778 4.311096e-07 2.425178e-05
## FBN2        2298.65634      0.9271437 0.16349007 1.479995e-10 2.841006e-08
## AMIGO2        87.73563     -0.9021120 0.33424765 1.053664e-05 3.320065e-04
## SLC15A4      112.20080     -5.0520993 0.48001410 1.062696e-26 3.875918e-23
## SYT16        509.77658     -0.8876346 0.12284518 7.231588e-15 4.948901e-12
## FBLN5        392.69902     -0.5983426 0.25039899 8.434588e-05 1.716209e-03
## DISP2        928.92284     -0.6852023 0.15380296 5.194077e-08 4.052213e-06
## CELF6        533.45696     -0.6125166 0.15407709 4.679679e-07 2.566611e-05
## SLC16A3      183.44445     -0.6384142 0.28540993 9.889874e-05 1.931504e-03
## SEMA6C      1542.25573     -0.6840026 0.07433479 2.557235e-22 4.663437e-19
## TMEM108      210.89728     -0.8748787 0.21141470 1.785678e-07 1.132664e-05
## OCIAD2       149.17437     -0.6805368 0.29003243 6.336283e-05 1.355426e-03
## MARCHF1      629.68634     -0.9650702 0.20138525 1.112114e-08 1.074479e-06
## ADM           59.11124     -1.6387235 0.56888963 1.739127e-07 1.112055e-05
## NCAM1      15045.46948     -0.6040832 0.09989683 1.283758e-11 3.229094e-09
## HMGA2        821.36065      1.0684311 0.12470296 1.951475e-19 2.588188e-16
## DLG2         494.01385     -0.8853535 0.13421138 5.325995e-13 2.220027e-10
## MFSD6        246.14968     -0.7333488 0.15721902 1.944913e-08 1.784549e-06
## GLT1D1        21.05085     -5.7269040 1.13401425 1.829680e-08 1.689443e-06
## TMEM132D      29.40525     -6.9913956 1.15043083 5.982587e-11 1.246857e-08
## NRSN1        402.78754     -0.8401904 0.20873777 2.826042e-07 1.682822e-05
## DAB2          53.97830      0.8421024 0.33041481 1.923820e-05 5.397425e-04
## PID1         580.87020     -0.8756672 0.16503355 9.727390e-10 1.414488e-07
## CABYR         94.08751     -0.7397264 0.24448804 9.013170e-06 2.941681e-04
## ANKRD29      176.45918     -0.8484308 0.27057725 4.767036e-06 1.795058e-04
## ROBO3      11317.98063     -0.6337081 0.22892312 2.662751e-05 6.913515e-04
## GPR26        150.22513     -1.0907805 0.31939121 7.595748e-07 3.888223e-05
## ADAMTS1      141.06621      0.6390167 0.41598680 2.674760e-04 4.120599e-03
## PPP2R2B     1211.96384     -0.7428250 0.11576922 1.084261e-12 4.055971e-10
## SLC6A1       752.29630     -0.6983533 0.15808080 6.056844e-08 4.531451e-06
## SYN2         141.47105     -0.8848304 0.21189600 1.531648e-07 9.843704e-06
## LDLRAP1      143.16822      0.6743081 0.17908754 9.057283e-07 4.540780e-05
## NRG2          88.19297     -0.7916451 0.25523028 6.248050e-06 2.211126e-04
## SPTBN4       298.68420     -0.6580827 0.16072756 2.559546e-07 1.555884e-05
## CELF5       2194.90201     -0.6548599 0.11297262 4.981540e-11 1.101147e-08
## ALPL         309.27324      0.7535060 0.24097777 6.473436e-06 2.259353e-04
## B3GALT2      170.10870     -0.5898160 0.26679369 1.345099e-04 2.465282e-03
## INAVA        332.20664      0.7521482 0.13006808 5.536428e-11 1.170593e-08
## EDIL3        757.13929     -0.6231910 0.17082964 1.594858e-06 7.433668e-05
## GPX8         401.52284      0.6172509 0.12604680 7.351421e-09 7.771731e-07
## GRIK2        299.13014     -0.7098055 0.24162197 1.266858e-05 3.842452e-04
## GPR85        366.36805     -0.7125679 0.23547227 9.747524e-06 3.132305e-04
## ADCY1       4192.59841     -0.9742540 0.16570794 4.656809e-11 1.045203e-08
## DIRAS2       491.64407     -1.2545762 0.25280186 9.441800e-10 1.405576e-07
## LRFN5        239.88452     -0.7555097 0.20975036 1.423091e-06 6.697250e-05
## DACT1        702.59990     -0.7116622 0.19975641 1.757110e-06 7.999251e-05
## SCN3B       2362.58124     -0.6462085 0.10394527 3.857663e-12 1.125589e-09
## CYYR1         73.19137      0.9760850 0.22178162 5.484314e-08 4.189040e-06
## IFTAP        149.45787      3.8149250 0.83819006 4.503828e-08 3.590511e-06
## PRTG        3103.66116      0.8499776 0.33579134 1.912060e-05 5.374768e-04
## ZNF667-AS1   190.70671     -1.5692075 0.28796471 2.009081e-12 6.106351e-10
## CACNG2        91.00247     -0.7446820 0.32268174 5.024199e-05 1.143495e-03
## PBX3        5969.08525     -0.7478592 0.18667067 3.253133e-07 1.906023e-05
## ATCAY       3924.16315     -0.6430030 0.07755912 8.689485e-19 1.056424e-15
## HID1         551.38951     -0.5891564 0.11867937 5.817576e-09 6.381400e-07
## LDLRAD4      283.47799     -0.7504070 0.18458666 2.573769e-07 1.558038e-05
## NSG1        2945.24998     -0.6237349 0.15912878 5.645101e-07 3.005707e-05
## FAM110B      388.99118     -0.7000124 0.16057412 7.816056e-08 5.644972e-06
## B3GALNT1     197.27852     -1.2322636 0.28435719 1.589165e-08 1.505475e-06
## KCNAB1        37.03410     -0.6230889 0.39765713 2.999243e-04 4.497016e-03
## PROKR1       100.84072     -0.6275923 0.36503876 2.565635e-04 3.994670e-03
## TMEM266       62.33998     -0.8849505 0.26730724 2.621942e-06 1.115204e-04
## FAM153A       19.36876     -0.7267146 0.60581420 1.287271e-04 2.383248e-03
## NSG2        9145.93140     -0.7988035 0.12241877 6.319986e-13 2.561174e-10
## KSR2         454.26454     -0.6349085 0.14800428 1.180848e-07 7.938890e-06
## CDK5R2       254.97786     -0.6014570 0.19289849 1.057980e-05 3.326482e-04
## DSCAM        208.44759     -0.8230481 0.23509266 1.760066e-06 7.999251e-05
## NEGR1       1444.14733     -0.7479014 0.19680797 7.105949e-07 3.715724e-05
## ABLIM3       450.82719     -0.9006466 0.17580665 2.487179e-09 3.182934e-07
## CHST1        713.47635     -0.6925463 0.25186407 2.249570e-05 6.055162e-04
## CREG2        138.74220     -0.7569511 0.21705381 2.089323e-06 9.208802e-05
## CDK5R1      3338.39565     -0.6056326 0.09483985 1.496095e-12 4.967027e-10
## GRIN1        222.51507     -1.0364348 0.29876100 8.991291e-07 4.523239e-05
## FIBIN         51.00988     -1.0956181 0.38620641 2.685837e-06 1.125968e-04
## NHLH2        732.17858     -1.4226892 0.34224767 5.380537e-09 5.992110e-07
## PCDHB9       184.02553     -0.6974683 0.16436313 1.291169e-07 8.447023e-06
## TMEM151A     113.80417     -0.6928371 0.29070319 5.513640e-05 1.231830e-03
## ZNF154       134.99483     -0.8498836 0.40211347 3.748764e-05 9.084379e-04
## NRXN1       1525.03327     -0.6163013 0.19590145 9.152625e-06 2.973890e-04
## ARHGAP45     528.36201      0.7734520 0.20840832 9.477212e-07 4.718875e-05
## H2AW         274.69296     -0.8976449 0.16669333 6.628125e-10 1.039760e-07
## KCNH8       1733.32830     -0.5934288 0.22802656 4.980784e-05 1.137162e-03
## KCNQ3        412.98841     -1.3393723 0.30165665 3.806476e-09 4.551859e-07
## RALYL        267.28271     -1.2637986 0.42815375 7.571616e-07 3.888223e-05
## SEPTIN5     1728.57986     -0.6958817 0.08509777 2.137494e-18 2.227421e-15
## ANKS1B      1016.40814     -0.8213030 0.26596678 5.921479e-06 2.123333e-04
## PDIA2        329.84095     -0.6198965 0.14449716 1.229487e-07 8.153177e-06
## KCNIP4        65.59152     -0.8022625 0.44207196 6.954168e-05 1.474627e-03
## IKZF1        251.05625      0.6860593 0.14888563 2.580493e-08 2.267880e-06
## ZNF829        93.65336     -1.0039638 0.27083531 5.390929e-07 2.891480e-05
## MYT1L       1171.33178     -0.8328617 0.17439805 1.234753e-08 1.185119e-06
## MAPT        7145.21800     -0.6342886 0.12942554 6.871555e-09 7.371258e-07
## C3orf70      232.29264     -0.6099549 0.24280747 5.863218e-05 1.290173e-03
## VWC2          65.85703     -0.8657934 0.39660172 3.101271e-05 7.787339e-04
## SEMA4A       393.40997     -0.6650841 0.12693169 1.125380e-09 1.578670e-07
## ZNF471       418.29083     -1.2525006 0.27224540 4.635940e-09 5.367756e-07
## ZNF605       821.23079     -0.9315395 0.08671207 1.678997e-28 8.164965e-25
## H2BU1         51.80292     -0.7910088 0.34443311 4.021115e-05 9.632849e-04
## ZNF100       317.72841     -0.8158987 0.13372901 9.759601e-12 2.542550e-09
## COL4A6       431.55589      0.8398355 0.30257889 1.200534e-05 3.678545e-04
## DNM3         783.57924     -0.6756933 0.14743270 2.930906e-08 2.500525e-06
## ZNF667       175.36693     -1.8427466 0.35562436 1.770434e-12 5.614969e-10
## CACNA1E      874.52491     -1.0562702 0.14783576 1.312793e-14 7.980141e-12
## TUSC1         90.27037     -0.9239695 0.35984837 1.201371e-05 3.678545e-04
## LRRTM3        91.32120     -0.6489274 0.42623518 2.478091e-04 3.912648e-03
## PLXNB3       186.04240     -0.8685307 0.30423212 8.850380e-06 2.914124e-04
## ZNF525       143.24205     -0.6845472 0.20877895 4.840865e-06 1.806224e-04
## GP1BB        175.33389     -0.8974986 0.16519123 5.157133e-10 8.267848e-08
## LINC02487    105.40628     -1.5255749 0.81777030 3.609727e-06 1.415653e-04
## PCDHA5        81.91158     -0.7255426 0.23454020 7.708863e-06 2.623469e-04
## PCDHA4      1036.58113     -0.9736976 0.10501985 4.476157e-22 7.255850e-19
## PCDHA2       319.06314     -4.6839904 0.35063185 2.270822e-41 1.656451e-37
## TRIM71      1221.68580      0.7256423 0.29858037 4.276687e-05 1.009589e-03
## XKR4         883.11247     -0.6476978 0.14470422 5.020401e-08 3.937776e-06
## MIR219A2HG   311.47484      0.6971330 0.25104478 2.057505e-05 5.695814e-04
## MEG3        7371.75115     -9.0930050 0.60523993 3.161204e-52 4.611880e-48
## SKOR2        374.49058     -2.6468019 0.81651045 1.302233e-07 8.481376e-06
## GPC1-AS1      53.44658     -0.6426524 0.31171542 1.382371e-04 2.511507e-03
## MEG9          29.44203     -7.0978054 0.96256893 7.462871e-15 4.948901e-12
## LINC02470     47.22127     -7.5383128 1.09173670 2.128254e-13 1.063141e-10
## MEG8          62.24677     -2.2602300 0.49687695 2.029972e-10 3.641494e-08
## LINC01515     75.01665     -3.0635122 0.40975071 5.632265e-15 4.324690e-12
## FEZF1-AS1     31.11261      0.8876431 1.09961696 9.187024e-05 1.833509e-03
##  [ reached 'max' / getOption("max.print") -- omitted 16 rows ]

Complete DEG List

Already filtered DEGs from DEA

DEA <- list(D0_HT = row.names(DEAList_ips_HT$HT$DEGs),
            D0_AR = row.names(DEAList_ips_AR$AR$DEGs),
            D25_HT = row.names(DEAList_day25_HT$HT$DEGs), 
            D25_AR = row.names(DEAList_day25_AR$AR$DEGs),
            D50_HT = row.names(DEAList_day50_HT$HT$DEGs), 
            D50_AR = row.names(DEAList_day50_AR$AR$DEGs))

lapply(DEA, length)
## $D0_HT
## [1] 2574
## 
## $D0_AR
## [1] 25
## 
## $D25_HT
## [1] 1511
## 
## $D25_AR
## [1] 111
## 
## $D50_HT
## [1] 2202
## 
## $D50_AR
## [1] 652

Manual filtering of DEGs

Res <- list(D0_HT = DEAList_ips_HT$HT$res, 
            D0_AR = DEAList_ips_AR$AR$res,
            D25_HT = DEAList_day25_HT$HT$res, 
            D25_AR = DEAList_day25_AR$AR$res,
            D50_HT = DEAList_day50_HT$HT$res,
            D50_AR = DEAList_day50_AR$AR$res)

Res <- lapply(Res, as.data.frame)

Res$D0_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D0_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D25_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D25_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D50_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D50_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)

3. Scatterplots

iPSCs

#Extract Results 
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD0 <- computeCompResFC(Res$D0_HT, Res$D0_AR) 
## The number of genes in the first data set is 16981
## The number of genes in the second data set is 16616
## The number of common genes that will be examined is 16616
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties
#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')

qDf <- lapply(quadr, {function(q) obj <- CompareResD0$Significant %>%
                                          dplyr::filter(Direction == q & Status == 'SignificantA&B') %>% 
                                          dplyr::select(genes, log2FoldChange_A, padj_A, 
                                                        log2FoldChange_B, padj_B, Log2FcSsum) %>%
                                          arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadr

Check DEGs overlap across time-point comparisons

compResFScatter(Res$D0_HT, Res$D0_AR)
## The number of genes in the first data set is 16981
## The number of genes in the second data set is 16616
## The number of common genes that will be examined is 16616
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties

Number of genes that are:

  • Up_Up 0
  • Down_Down: 10
  • Up_Down: 4
  • Down_Up: 1

Concordant Downregulated genes

qDf[['Down_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Discordant Upregulated and Downregulated genes

qDf[['Up_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Discordant Downregulated and Upregulated genes

qDf[['Down_Up']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Day25

#Extract Results 
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD25 <- computeCompResFC(Res$D25_HT, Res$D25_AR) 
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17781
## The number of common genes that will be examined is 17781
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties
#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')

qDf <- lapply(quadr, {function(q) obj <- CompareResD25$Significant %>%
                                          dplyr::filter(Direction == q & Status == 'SignificantA&B') %>% 
                                          dplyr::select(genes, log2FoldChange_A, padj_A, 
                                                        log2FoldChange_B, padj_B, Log2FcSsum) %>%
                                          arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadr

Check DEGs overlap across time-point comparisons

compResFScatter(Res$D25_HT, Res$D25_AR)
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17781
## The number of common genes that will be examined is 17781
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties

Number of genes that are:

  • Up_Up 7
  • Down_Down: 9
  • Up_Down: 5
  • Down_Up: 2

Concordant Upregulated genes

qDf[['Up_Up']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Concordant Downregulated genes

qDf[['Down_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Discordant Upregulated and Downregulated genes

qDf[['Up_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Day50

#Extract Results 
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD50 <- computeCompResFC(Res$D50_HT, Res$D50_AR) 
## The number of genes in the first data set is 17673
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17673
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties
#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')

qDf <- lapply(quadr, {function(q) obj <- CompareResD50$Significant %>%
                                          dplyr::filter(Direction == q & Status == 'SignificantA&B') %>% 
                                          dplyr::select(genes, log2FoldChange_A, padj_A, 
                                                        log2FoldChange_B, padj_B, Log2FcSsum) %>%
                                          arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadr

Check DEGs overlap across time-point comparisons

compResFScatter(Res$D50_HT, Res$D50_AR)
## The number of genes in the first data set is 17673
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17673
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties

Number of genes that are:

  • Up_Up 9
  • Down_Down: 9
  • Up_Down: 49
  • Down_Up: 9

Concordant Upregulated genes

qDf[['Up_Up']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Concordant Downregulated genes

qDf[['Down_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Discordant Upregulated and Downregulated genes

qDf[['Up_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Discordant Downregulated and Upregulated genes

qDf[['Down_Up']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Day25 Heterozygous and Day50 Ancestral

#Extract Results 
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD25ht_50ar <- computeCompResFC(Res$D25_HT, Res$D50_AR) 
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17116
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties
#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')

qDf <- lapply(quadr, {function(q) obj <- CompareResD25ht_50ar$Significant %>%
                                          dplyr::filter(Direction == q & Status == 'SignificantA&B') %>% 
                                          dplyr::select(genes, log2FoldChange_A, padj_A, 
                                                        log2FoldChange_B, padj_B, Log2FcSsum) %>%
                                          arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadr

Check DEGs overlap across time-point comparisons

compResFScatter(Res$D25_HT, Res$D50_AR)
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17116
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties

Number of genes that are:

  • Up_Up 11
  • Down_Down: 13
  • Up_Down: 23
  • Down_Up: 3

Concordant Upregulated genes

qDf[['Up_Up']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Concordant Downregulated genes

qDf[['Down_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

Concordant Downregulated genes

qDf[['Up_Down']]%>% 
  DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons', 
                options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))

4. upsetR

Check DEGs overlap across time-point comparisons.

Heterozygous

upset(fromList(DEA[c(1,3,5)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
      keep.order = T, main.bar.color='grey10',
      decreasing = T, 
      mb.ratio = c(0.6, 0.4),
      text.scale = 1, 
      point.size = 3, 
      line.size = 1)

Ancestral

upset(fromList(DEA[c(2,4,6)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
      keep.order = T, main.bar.color='grey10',
      decreasing = T, 
      mb.ratio = c(0.6, 0.4),
      text.scale = 1, 
      point.size = 3, 
      line.size = 1)

All organoids

upset(fromList(DEA[c(3,4,5,6)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
      keep.order = T, main.bar.color='grey10',
      decreasing = T, 
      mb.ratio = c(0.6, 0.4),
      text.scale = 1, 
      point.size = 3, 
      line.size = 1)

All samples

upset(fromList(DEA), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
      keep.order = T, main.bar.color='grey10',
      decreasing = T, 
      mb.ratio = c(0.6, 0.4),
      text.scale = 1, 
      point.size = 3, 
      line.size = 1)

5. Venn diagram

venn_plot <- ggvenn(DEA[3:6], show_elements=FALSE, fill_alpha = 0.2, text_size = 4, show_percentage = FALSE, fill_color = c('#FFDAB9', '#80CBC4', '#A0E8A9', '#C8A2C8'))

venn_plot

ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'VennPlotOrganoids_1.pdf'))
## Saving 8 x 10 in image
venn_plot <- ggvenn(DEA[3:6], show_elements=FALSE, fill_alpha = 0.2, text_size = 4, show_percentage = FALSE, fill_color = c('#FFDAB9', '#80CBC4', '#FFDAB9', '#80CBC4' ))

venn_plot

ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'VennPlotOrganoids_2.pdf'))
## Saving 8 x 10 in image

6. Intersection identities

v.table <- venn(DEA[3:6])


all_intersections <- attr(v.table, "intersections")

for (comparison in names(all_intersections)) {
      cat(comparison, "\n")
      print(all_intersections[[comparison]])
}
## D25_AR:D50_AR 
##  [1] "FZD10"     "TFCP2"     "SLC15A4"   "TPPP3"     "PFKFB3"    "H2AW"      "BCAM"     
##  [8] "ZNF605"    "ZNF100"    "PCDHA4"    "PCDHA13"   "FZD10-AS1" "LHX1"      "LHX1-DT"  
## D25_AR:D50_HT 
## [1] "DSG2"    "GPR50"   "CLU"     "LMO2"    "GRIA1"   "PPP1R32" "SERINC5" "CRABP1" 
## D25_HT:D25_AR 
##  [1] "BMP7"           "BMF"            "DNAI1"          "SSUH2"          "MNS1"          
##  [6] "LEF1"           "HDC"            "MYBPC1"         "BLOC1S5-TXNDC5" "TXNIP"         
## D25_HT:D50_AR 
##  [1] "RUNX1T1"      "SORBS1"       "EEF1A2"       "PCYT1B"       "SEMA5A"       "CDH9"        
##  [7] "RBP1"         "FNDC4"        "BCL11A"       "NXPH1"        "MMP24"        "NOTCH2"      
## [13] "STK26"        "TNS3"         "ARHGAP24"     "AMIGO2"       "COL2A1"       "DISP2"       
## [19] "CCDC33"       "KIFC3"        "GAS8"         "CRABP2"       "HMGCLL1"      "GRM1"        
## [25] "ANKRD29"      "ROBO3"        "ADAMTS1"      "VCAM1"        "UNCX"         "EFNA1"       
## [31] "DSCAM"        "NEGR1"        "SLITRK1"      "BACE2"        "OAF"          "HS6ST3"      
## [37] "CPNE4"        "LRRTM3"       "C2orf72"      "ARHGEF35-AS1"
## D25_HT:D50_HT 
##   [1] "HS3ST1"      "KLHL13"      "SKAP2"       "GCFC2"       "CRLF1"       "TMEM132A"   
##   [7] "DNAH9"       "GAS7"        "TKTL1"       "CAMK1G"      "NFIX"        "TENM1"      
##  [13] "MTMR11"      "ATP1A2"      "ZNF582"      "CD74"        "ADGRA2"      "FAS"        
##  [19] "TMSB10"      "COL9A2"      "FOXC1"       "PARP12"      "PRDM6"       "NGFR"       
##  [25] "ME1"         "TGFBR3"      "FGF10"       "NCK2"        "SPEG"        "ST6GAL1"    
##  [31] "ZNF37A"      "PAX2"        "MCAM"        "ADCY2"       "SESN1"       "LYRM2"      
##  [37] "EFR3B"       "PPEF1"       "BAX"         "ADAMTS2"     "GNAO1"       "SLC4A11"    
##  [43] "LAMB1"       "WDR76"       "COL9A3"      "COMT"        "CYP26A1"     "MFNG"       
##  [49] "LGALS1"      "SOX10"       "TIMP3"       "RIN3"        "DHRS2"       "SLCO4A1"    
##  [55] "RNF125"      "TIMP1"       "SYTL4"       "FGF9"        "DGKH"        "MAPK3"      
##  [61] "GDPD3"       "TRPA1"       "SLC1A6"      "TFPI2"       "LHX2"        "ENG"        
##  [67] "SH3GL2"      "RASSF4"      "TLX1"        "SFXN3"       "PNPO"        "SOX6"       
##  [73] "TNS2"        "ELK3"        "OAS3"        "MDGA1"       "KHDRBS2"     "ASCC3"      
##  [79] "PCDHB5"      "CDH6"        "PDGFRB"      "UNC5A"       "EHHADH"      "MRPL3"      
##  [85] "POMC"        "ITGA4"       "HPCAL1"      "QPCT"        "DLX2"        "PRRX1"      
##  [91] "KIF21B"      "ZNHIT6"      "SLC2A1"      "NENF"        "PROX1"       "NRP2"       
##  [97] "RAB32"       "ONECUT2"     "PYROXD2"     "ACAT2"       "KIAA1217"    "EGR1"       
## [103] "TNFRSF10B"   "CAT"         "ARL4A"       "GLIPR2"      "PLP1"        "CDKN1A"     
## [109] "MT2A"        "TNFSF9"      "CITED1"      "FLRT1"       "PLEKHG3"     "TMEM35A"    
## [115] "LRRC61"      "GNG11"       "RASL11B"     "LIF"         "DOCK4"       "FEZF1"      
## [121] "ISLR"        "LOXL1"       "E2F8"        "SOX15"       "CD68"        "MTUS1"      
## [127] "RPS4Y1"      "GAMT"        "GDPD2"       "SH3BP4"      "COL5A1"      "MED18"      
## [133] "HIP1R"       "PNCK"        "DUSP9"       "EDA2R"       "RAB11FIP4"   "SLC6A6"     
## [139] "GFPT2"       "SLC6A11"     "NUP210"      "RAP1GAP2"    "BCAN"        "PPP1R3D"    
## [145] "DCLK1"       "POSTN"       "STARD13"     "NTS"         "SWAP70"      "RNF122"     
## [151] "CAMK1"       "SYT6"        "CMPK2"       "DAGLA"       "ADAM19"      "BICDL1"     
## [157] "MDM2"        "SP110"       "SERPINE2"    "DRAM1"       "GPNMB"       "GAD2"       
## [163] "CTSV"        "MYC"         "TFAP2A"      "FOXF2"       "SLCO5A1"     "ITGA11"     
## [169] "ZNF280D"     "IFI44L"      "IFI44"       "SIX3"        "ZNF365"      "STAT4"      
## [175] "HECW2"       "PARP9"       "SEMA7A"      "HERC5"       "CPNE8"       "FOXN4"      
## [181] "GRTP1"       "ARMH4"       "NEIL1"       "ST8SIA2"     "TIGD7"       "MAPK4"      
## [187] "STAC2"       "PLPP2"       "PGGHG"       "HMCN1"       "CGN"         "EFNA3"      
## [193] "CNGA3"       "SLC4A10"     "DLX1"        "SPAG16"      "ITGA9"       "IGFBP3"     
## [199] "DIAPH2"      "RGS20"       "STOM"        "LCN9"        "PROSER2"     "PAOX"       
## [205] "RGS10"       "CDH8"        "GPM6A"       "FREM2"       "TMEM86A"     "ABTB3"      
## [211] "GFRA1"       "TRIM36"      "PLEKHH2"     "ZNF117"      "RASSF3"      "NMRAL1"     
## [217] "LGI4"        "UBASH3B"     "PITPNC1"     "OBSCN"       "DKK2"        "PTPRN2"     
## [223] "AFF2"        "WIF1"        "MPV17L"      "MMP14"       "C2CD2"       "PSMG3"      
## [229] "XKR8"        "CLSTN2"      "SLC13A3"     "DMTN"        "S100B"       "LY6E"       
## [235] "FDXR"        "ZNF75A"      "AK4"         "NFIA"        "DDR2"        "SPATA18"    
## [241] "TAFA4"       "CDS1"        "PTX3"        "APBB2"       "DTX3L"       "PRKCD"      
## [247] "ARHGEF3"     "EXO5"        "ERMAP"       "ITGA2"       "F2RL2"       "CMBL"       
## [253] "EGFLAM"      "UBLCP1"      "ACSL6"       "DLC1"        "SPIDR"       "VEGFD"      
## [259] "PHOX2A"      "PKNOX2"      "E2F7"        "PACSIN3"     "KCNC2"       "ADAMTS15"   
## [265] "IKBIP"       "ALKBH3"      "TMEM100"     "CHRFAM7A"    "ELFN2"       "GREM1"      
## [271] "TUBA1C"      "ZNF528"      "PLIN4"       "RAB3IL1"     "SCARA3"      "MMADHC"     
## [277] "COL3A1"      "GFRA2"       "INPP5D"      "CHST14"      "PCSK9"       "KCNK9"      
## [283] "ONECUT1"     "GPRC5C"      "EMB"         "SIX2"        "DLGAP1"      "POLH"       
## [289] "PRKCE"       "NPTX1"       "CLCN5"       "DSEL"        "ZNF562"      "ECEL1"      
## [295] "GATM"        "CFAP46"      "PRNP"        "FRMD5"       "FRMD3"       "ZMAT3"      
## [301] "ZNF596"      "RARG"        "MYD88"       "ZNF680"      "PARP14"      "PTPRM"      
## [307] "VEGFB"       "TNFRSF10C"   "JUP"         "HAP1"        "CTSF"        "MSRB3"      
## [313] "PHLDA3"      "ZNF25"       "ALG10B"      "FOSL1"       "MTLN"        "TUBB6"      
## [319] "ZNF135"      "HSD11B2"     "RIMS2"       "RNF152"      "BDNF"        "BOK"        
## [325] "TCERG1L"     "TCIM"        "KCNA3"       "ANXA2R"      "ANXA2R-OT1"  "ZNF619"     
## [331] "ZNF454"      "POGLUT3"     "NRIP1"       "TSPYL5"      "ZFP3"        "ARSJ"       
## [337] "FAM83H"      "AEN"         "TMEM132E"    "TMIE"        "ZNF875"      "CHST15"     
## [343] "KCNIP1"      "PLCB1"       "RNF32-DT"    "SPNS2"       "CHST6"       "MAGEA2B"    
## [349] "CCDC125"     "BCOR"        "FHL3"        "TRIM61"      "ZNF703"      "ANKRD45"    
## [355] "CFAP91"      "PNMA3"       "ZNF730"      "TBX1"        "CNTN2"       "ALDH1A3"    
## [361] "CSF1"        "TXNRD2"      "LRRC26"      "SRY"         "TMEM121"     "RPS27L"     
## [367] "INPP5J"      "AHNAK2"      "OLFML2A"     "NDUFA4L2"    "PRAME"       "C11orf87"   
## [373] "IFIT1"       "RTN4RL1"     "SHOX"        "ZNF225-AS1"  "ANKRD37"     "ZNF501"     
## [379] "HPDL"        "PDZD7"       "WDR86"       "SAMD11"      "POTEE"       "PRELP"      
## [385] "SHISA6"      "H1-0"        "SP6"         "PLAC9"       "ZNF527"      "ZNF33A"     
## [391] "PAX8-AS1"    "FAM217B"     "ZNF107"      "NTNG2"       "ARL9"        "CACNA1H"    
## [397] "AJAP1"       "POTEF"       "ZNF502"      "POTEI"       "ARID5A"      "ZNF585A"    
## [403] "ZNF138"      "ZNF429"      "ZNF470"      "ADARB1"      "PDGFA"       "EME2"       
## [409] "H2BC12"      "HES5"        "ZNF71"       "ZNF560"      "ZNF273"      "ZNF248"     
## [415] "HOXC4"       "ZNF583"      "ZNF534"      "EIF1AY"      "INPP5F"      "CCDC152"    
## [421] "CSAG1"       "TCEAL5"      "HSPA1A"      "HLA-C"       "INSYN2B"     "PNMA8B"     
## [427] "LRRC10B"     "MUC19"       "C21orf62"    "GOLGA8O"     "HLA-A"       "GPX3"       
## [433] "MAGEA12"     "ERV3-1"      "EMP2"        "LTB4R"       "FAM66B"      "SCRT2"      
## [439] "HMX1"        "LINC01139"   "LINC03010"   "CEBPZOS"     "LINGO3"      "LINC02076"  
## [445] "EBF2"        "PLXNA4"      "ZNF880"      "POTEM"       "ADM5"        "MIR3659HG"  
## [451] "LINC01980"   "RUSC1-AS1"   "LINC01748"   "SOX21-AS1"   "MIR34AHG"    "ZBTB46-AS2" 
## [457] "PSMG3-AS1"   "TSPAN19"     "GOLGA8N"     "LNCTAM34A"   "HLA-B"       "DANT2"      
## [463] "GNAS-AS1"    "FAM88E"      "FOXD2-AS1"   "SHISA9"      "LINC00649"   "PCDHGC3"    
## [469] "NECTIN3-AS1" "PDE6B-AS1"   "SOX2-OT"     "ZNF512"      "PTCHD4"      "NEAT1"      
## [475] "LINC00682"   "SLCO5A1-AS1" "MIR4458HG"   "CASC9"       "LINC02972"   "PVT1"       
## [481] "GOLGA8K"     "AGA-DT"      "CHCHD10"     "YPEL3-DT"    "LINC00491"   "LINC02600"  
## [487] "LINC02315"   "FOXD1"       "ZFHX4-AS1"   "PCDHGA10"    "PCDHGB4"     "AP5B1"      
## [493] "SALL3"       "LINC02306"   "DIO3OS"      "LINC02301"   "LINC02820"   "TMEM179"    
## [499] "ZNF710-AS1"  "PWRN1"       "SPON1"       "LINC01896"   "PARD6G-AS1"  "KC6"        
## [505] "ZNF285"      "MAGEA2"      "CSAG3"       "MIA-RAB4B"   "ZNF470-DT"   "LINC01297"  
## [511] "TUBGCP5"    
## D50_HT:D50_AR 
##   [1] "PRKAR2B"    "ITGA3"      "TAC1"       "SYT13"      "CPS1"       "TNFRSF1B"   "FLT4"      
##   [8] "CAMK2B"     "SEZ6"       "FGFR2"      "PRKCZ"      "ATP2B3"     "REEP1"      "RORA"      
##  [15] "LNX1"       "PPP2R2C"    "TRIP6"      "PUS7"       "MYH7"       "FKBP5"      "CACNA1I"   
##  [22] "GINS1"      "SALL4"      "SLC32A1"    "MAP1LC3A"   "NOL4"       "HSF4"       "CBLN1"     
##  [29] "ICAM5"      "PLA2G4C"    "PLEKHA4"    "ADAP1"      "CHN2"       "TFR2"       "RARRES2"   
##  [36] "EBF3"       "NEIL3"      "CRYAB"      "GMNN"       "ARFGEF3"    "HBEGF"      "GABRG2"    
##  [43] "HES1"       "SLC5A7"     "DNAJC6"     "PADI2"      "CA14"       "ATP10B"     "IQSEC3"    
##  [50] "MND1"       "SV2C"       "GRM4"       "PACSIN1"    "MIR9-1HG"   "OPRL1"      "BCL2L12"   
##  [57] "HIVEP3"     "TUBA4A"     "CDKN2D"     "EGLN3"      "CBFA2T3"    "GINS2"      "LIN28A"    
##  [64] "TRIM22"     "GPR12"      "MYBPH"      "ALDH1L2"    "GABBR2"     "ARHGEF39"   "PAK6"      
##  [71] "STRA6"      "CYP2C8"     "PCDH10"     "RASGEF1B"   "MTTP"       "RTN1"       "FBLN5"     
##  [78] "NOL3"       "RHBDL3"     "TAF4B"      "SLC16A3"    "CBLN2"      "SUSD4"      "ST6GAL2"   
##  [85] "SCN1A"      "CDCA7"      "MARCHF4"    "VWA5B2"     "OCIAD2"     "MARCHF1"    "SFRP2"     
##  [92] "PSD2"       "EML3"       "CNTN5"      "LYPD1"      "VEGFC"      "ADAMTS12"   "CCDC3"     
##  [99] "AKR1C2"     "STK32B"     "JAKMIP1"    "PID1"       "CDH12"      "GPR26"      "CNTNAP5"   
## [106] "GOLGA7B"    "PPP2R2B"    "SLC6A1"     "LDLRAP1"    "NPM2"       "CPAMD8"     "GPATCH4"   
## [113] "ALPL"       "GPX8"       "GPR85"      "MYORG"      "DIRAS2"     "LRFN5"      "AMER2"     
## [120] "RET"        "BTNL9"      "CDYL2"      "PRTG"       "YPEL4"      "LDLRAD4"    "NSG1"      
## [127] "FSTL5"      "B3GALNT1"   "KCNAB1"     "PROKR1"     "PCDH7"      "KCNK3"      "KCND3"     
## [134] "CDK5R2"     "CALB2"      "CKS1B"      "ABLIM3"     "IGDCC3"     "DPP10"      "CREG2"     
## [141] "CDK5R1"     "LY6H"       "FIBIN"      "DSCAML1"    "NHLH2"      "AURKB"      "FAM216B"   
## [148] "ARHGAP45"   "HHIPL1"     "CALN1"      "CHEK2"      "KCNQ3"      "PCDH9"      "POU6F1"    
## [155] "MAP7D2"     "ANKS1B"     "GPRIN3"     "PARPBP"     "SYN3"       "DLEU7"      "MYT1L"     
## [162] "MAPT"       "LUZP2"      "LIN28B"     "DIPK1C"     "DNER"       "JAKMIP3"    "INSYN2A"   
## [169] "RASSF10"    "PTPRT"      "SEMA4A"     "SLC6A9"     "SLC6A17"    "ADGRA1"     "DIO3"      
## [176] "NUP62CL"    "CACNA1E"    "HYLS1"      "TUSC1"      "SMOC1"      "PLXNB3"     "GRM3"      
## [183] "INF2"       "LINC02487"  "COL15A1"    "PCDHA7"     "MIR219A2HG" "C2orf74-DT" "SYT3"      
## [190] "LCNL1"      "SP9"        "INHBA-AS1"  "LINC02470"  "RFPL1S"     "LINC01503"  "LINC01322" 
## [197] "PCP4L1"     "EPHA5-AS1"  "PCDHGB7"    "TMPO-AS1"   "LINC01619"  "FIGNL2"     "GRIN2B"    
## [204] "EPOP"      
## D25_AR:D50_HT:D50_AR 
## [1] "ZNF506"     "ZNF671"     "UNC5B"      "LRRC4C"     "GLT1D1"     "ZNF585B"    "ZNF790-AS1"
## D25_HT:D25_AR:D50_HT 
##  [1] "CACNA1G"   "RSPO3"     "VAX1"      "ANGPT1"    "ZNF558"    "LRRN3"     "SOX11"    
##  [8] "PCDH18"    "SILC1"     "PURPL"     "LINC02381" "BLACAT1"  
## D25_HT:D50_HT:D50_AR 
##  [1] "HECW1"      "CYP26B1"    "SYN1"       "ST3GAL1"    "MAMLD1"     "LRRC7"      "RIMBP2"    
##  [8] "GUCY1B1"    "ANKRD44"    "TRNT1"      "PCDHA6"     "SERTAD4"    "SLCO1A2"    "MLC1"      
## [15] "OLFM2"      "ACTA2"      "PTPN5"      "LAMA4"      "CHD5"       "NEK6"       "MSX2"      
## [22] "DNAJC15"    "CSMD2"      "MYRF"       "BCL11B"     "FOXP2"      "NFATC1"     "SH3BP5"    
## [29] "CTIF"       "PI15"       "MMRN1"      "NTRK3"      "CDH11"      "CACNA1A"    "RBMS3"     
## [36] "NKD2"       "LHFPL2"     "NFIB"       "FAM13C"     "ADM"        "CACNA1C"    "DAB2"      
## [43] "CA10"       "UNC5D"      "KIT"        "CACNA2D3"   "NRG2"       "CILP2"      "LMX1A"     
## [50] "KIF26B"     "INHBB"      "GUCY1A1"    "ZCCHC24"    "DACT1"      "CYYR1"      "RBFOX3"    
## [57] "FAM110B"    "PLEKHA2"    "NSG2"       "TNFRSF10D"  "UCP2"       "GRIN1"      "RNF182"    
## [64] "COL18A1"    "KCNH8"      "SEPTIN5"    "FAM183A"    "C3orf70"    "LITAF"      "MYT1"      
## [71] "TMEM229B"   "MMP17"      "GP1BB"      "NPTXR"      "CYP4F26P"   "FEZF1-AS1"  "ANKRD18B"  
## [78] "LINC01122"  "MIR210HG"   "PCDHA10"    "LINC02506"  "ZNF528-AS1" "ARHGAP23"   "COPG2IT1"  
## D25_HT:D25_AR:D50_HT:D50_AR 
##  [1] "SPINK5"     "TRIM4"      "TMEM132D"   "IFTAP"      "ZNF667-AS1" "ZNF439"     "ZNF829"    
##  [8] "ZNF471"     "ZNF493"     "ZFP28"      "ZNF667"     "PCDHA2"     "MEG3"       "MEG9"      
## [15] "MEG8"       "LINC01515"  "PCDHA3"     "LINC02893"  "ZNF229"    
## D25_AR 
##  [1] "ZMYND10"   "NRXN3"     "UBE2T"     "OSBPL6"    "HSD17B14"  "PGK1"      "RND3"     
##  [8] "EGR2"      "P4HA1"     "APOE"      "ZFHX2"     "SPAG8"     "CFAP74"    "IGSF1"    
## [15] "B3GNT7"    "TMSB15B"   "RSPH1"     "ABHD6"     "DRC3"      "CNTNAP2"   "PDE12"    
## [22] "BNIP3"     "KCTD12"    "CFAP65"    "NKX2-5"    "GAS6"      "PDE4B"     "TPCN1"    
## [29] "LINC01551" "DNAJB13"   "CFAP43"    "MT-CYB"    "MT-ND2"    "MT-ND1"    "MT-ATP6"  
## [36] "FANK1"     "PRR29"     "MT-ATP8"   "MCIDAS"    "TNFRSF6B"  "MIR924HG" 
## D25_HT 
##   [1] "CFH"         "ENPP4"       "SEMA3F"      "COPZ2"       "TNFRSF12A"   "MYLIP"      
##   [7] "CDKL5"       "CELSR3"      "MAPK8IP2"    "PAX7"        "SEMA3G"      "CD4"        
##  [13] "TSPAN9"      "PLAUR"       "DCN"         "CLDN11"      "CCDC88C"     "BID"        
##  [19] "WWTR1"       "PHLDB1"      "MARCO"       "SNAI2"       "HGF"         "RUNX3"      
##  [25] "SERPINB1"    "ABCC2"       "ARNTL2"      "APBA2"       "TLL1"        "VCAN"       
##  [31] "RAI14"       "CDH10"       "RIPOR3"      "USH2A"       "ARAP2"       "LMO3"       
##  [37] "ELN"         "PPP1R3F"     "COL23A1"     "HOMER3"      "ALX4"        "LAMA3"      
##  [43] "PHPT1"       "PLEKHH1"     "SLC2A3"      "PSD"         "COL11A1"     "CDH3"       
##  [49] "TM7SF3"      "SNCAIP"      "SLC9A3R2"    "NTN1"        "ERBB3"       "ROPN1"      
##  [55] "PRKCQ"       "CTNNA2"      "TIE1"        "STAG3"       "CBFB"        "LAPTM4A"    
##  [61] "ST6GALNAC2"  "LMCD1"       "CDH19"       "SLC6A15"     "STK10"       "PANX2"      
##  [67] "PTGS2"       "MAP3K13"     "SEMA3C"      "FSCN1"       "SLC46A1"     "PAG1"       
##  [73] "CTTNBP2"     "CAPN6"       "ITGA8"       "SYNJ2"       "BRINP1"      "FKBP7"      
##  [79] "TNS1"        "MOXD1"       "DCT"         "COL5A3"      "MEF2C"       "AACS"       
##  [85] "OPRK1"       "SLC27A5"     "FAM234B"     "NKAIN1"      "COL16A1"     "PREP"       
##  [91] "ABCB1"       "WNT11"       "MMP2"        "SH3BP2"      "NID2"        "PHACTR3"    
##  [97] "TFAP2C"      "DOCK9"       "C3orf18"     "ARHGAP28"    "SMOX"        "FXYD5"      
## [103] "PITPNM2"     "CCDC80"      "CAPN3"       "TBX15"       "MAP3K1"      "PTGS1"      
## [109] "MYO3A"       "ITPR3"       "DSP"         "PCSK5"       "NRP1"        "HCN2"       
## [115] "MADCAM1"     "P2RX6"       "RBFOX2"      "IL2RB"       "SIX4"        "NINL"       
## [121] "NFATC2"      "CTSZ"        "COL20A1"     "CHRNA4"      "ISM1"        "PDYN"       
## [127] "PLCB4"       "MYL9"        "SAMHD1"      "MROH8"       "SNTA1"       "CDH20"      
## [133] "ATP11C"      "MCF2"        "SYP"         "ELF4"        "ASB9"        "KLHL4"      
## [139] "GABRE"       "RUBCNL"      "ACP5"        "FLT1"        "CRISPLD2"    "CRYM"       
## [145] "SLC6A2"      "LACTB"       "AP3B2"       "CTSH"        "ZDHHC2"      "CPQ"        
## [151] "CALB1"       "SFRP1"       "NIPAL2"      "PLAT"        "GSDMD"       "DNASE2"     
## [157] "KCNN1"       "DLX5"        "CPED1"       "PTPRZ1"      "PCOLCE"      "AHR"        
## [163] "PRUNE2"      "CORO2A"      "LHX6"        "SHB"         "CXCL12"      "LIPA"       
## [169] "NPM3"        "LGI1"        "SMARCD2"     "CCL2"        "PMP22"       "CRACD"      
## [175] "MAPK10"      "INPP4B"      "HGFAC"       "FAM149A"     "SIAE"        "CCND1"      
## [181] "CEP126"      "SLC15A3"     "TSPAN11"     "WNT5B"       "MANSC1"      "ARHGDIB"    
## [187] "ADGRD1"      "ENO2"        "COL12A1"     "GCNT2"       "FAM184A"     "SASH1"      
## [193] "PHACTR1"     "TRIM38"      "ADGRG6"      "MDFI"        "SMOC2"       "SLC29A1"    
## [199] "GHR"         "PCDHB15"     "NPR3"        "PRLR"        "PFKFB4"      "C3orf52"    
## [205] "ROPN1B"      "CISH"        "PEX5L"       "SPTBN1"      "FN1"         "KCNJ13"     
## [211] "EPHA4"       "TNR"         "OPRD1"       "KCNC4"       "DLGAP3"      "WLS"        
## [217] "OLFML3"      "NID1"        "HPCAL4"      "MFAP2"       "CDK18"       "FAAH"       
## [223] "PLPPR5"      "CNR1"        "MYB"         "FGF23"       "KLHL29"      "FKBP1B"     
## [229] "HOXB8"       "HOXB1"       "PCDHB10"     "TGFBI"       "GLT8D2"      "TBX2"       
## [235] "TMEM131L"    "TRIM6"       "PDZRN3"      "FMOD"        "HS3ST2"      "TWIST1"     
## [241] "CALD1"       "ITPR2"       "NECAB1"      "TNFAIP6"     "G0S2"        "FAM210B"    
## [247] "EDN3"        "PTGIS"       "PMEPA1"      "RUNX2"       "SH3TC1"      "BMP4"       
## [253] "SOX9"        "MIF4GD"      "EML2"        "TMEM74B"     "STAT5A"      "PRKCG"      
## [259] "SIX1"        "RHOJ"        "CANX"        "MASP1"       "PLAAT1"      "TNFRSF19"   
## [265] "ADM2"        "PODXL"       "LRRC17"      "CGNL1"       "RNASE1"      "STARD8"     
## [271] "CNN1"        "FAM98C"      "UNC13A"      "GDF15"       "H19"         "MNX1"       
## [277] "SHFL"        "GSE1"        "TMEM204"     "BARX1"       "RARA"        "MATN3"      
## [283] "TRIM5"       "SERPINF1"    "DDC"         "RIDA"        "HSPA12B"     "SYT11"      
## [289] "KANK4"       "BEX2"        "BEX1"        "ADCK2"       "LOXL2"       "MEIS2"      
## [295] "SPIRE1"      "TMEM106C"    "RSAD2"       "CRB1"        "SOX5"        "RERG"       
## [301] "SPX"         "DSC3"        "APLNR"       "PDGFRA"      "ETS1"        "TBX3"       
## [307] "KCP"         "KHDC1"       "MRAP2"       "ITGA7"       "AGAP2"       "HEY2"       
## [313] "TEC"         "SEMA4F"      "RAB11FIP5"   "NIBAN1"      "CHRND"       "FLNB"       
## [319] "TBC1D4"      "PHF11"       "LMO7"        "BZW2"        "ADAMTS7"     "SCN7A"      
## [325] "NIBAN2"      "ANGPTL2"     "LMX1B"       "ENPP2"       "IGFBPL1"     "KIAA0319"   
## [331] "SLC22A23"    "TUBB2A"      "CPEB2"       "FHDC1"       "ARRB1"       "SMAD6"      
## [337] "GCHFR"       "BCAR3"       "EMILIN1"     "ADAMTS14"    "MSTN"        "CDK15"      
## [343] "APH1B"       "CDKL2"       "CASP6"       "RGS3"        "PRICKLE1"    "LRIG3"      
## [349] "LUM"         "ASCL1"       "TMEM132B"    "FAM222A"     "ITGB7"       "REM2"       
## [355] "FRMD6"       "SORD"        "TLE3"        "DNAJA4"      "ARRDC4"      "CYP1A1"     
## [361] "ADAMTS17"    "HAPLN3"      "NKD1"        "ABCA8"       "GNAL"        "SLC13A5"    
## [367] "TMC6"        "TTYH2"       "COL6A1"      "COL6A2"      "ADAMTS10"    "SLC6A3"     
## [373] "FBN3"        "ARHGEF19"    "HSPG2"       "LMO4"        "IGSF3"       "ZNF697"     
## [379] "RXRG"        "ECM1"        "CTSK"        "KCNH1"       "OSR1"        "SFXN5"      
## [385] "GPR17"       "ZNF385B"     "UNC80"       "OSBPL10"     "CTDSPL"      "STAC"       
## [391] "COL8A1"      "NXPE3"       "STXBP5L"     "ATP10D"      "SNCA"        "MYO10"      
## [397] "PLK2"        "HAPLN1"      "PAM"         "MEGF10"      "ARHGAP26"    "GABRB2"     
## [403] "GFRA3"       "DAAM2"       "LRP12"       "CDKN2B"      "AOPEP"       "ADAM12"     
## [409] "ZNF215"      "PAMR1"       "KLHL35"      "TENM4"       "HTR3B"       "SCN2B"      
## [415] "KIAA1755"    "CLEC1A"      "PPP1R1C"     "C2orf50"     "ITPR1"       "GPR158"     
## [421] "THRB"        "NPAS3"       "PTPRO"       "EDNRA"       "FLI1"        "TLCD4"      
## [427] "PTPN14"      "TMEM163"     "TCF7L1"      "GUCY1A2"     "IGSF10"      "GJA1"       
## [433] "DYNLT5"      "PRDM8"       "BCL2L11"     "RBMS1"       "SCN3A"       "CNKSR3"     
## [439] "AK5"         "CHST9"       "PRKCA"       "LRRK1"       "ABCA5"       "C4orf19"    
## [445] "PDE1C"       "PLCL2"       "PPM1J"       "TTN"         "MMP16"       "ART3"       
## [451] "TSPAN7"      "FGF18"       "ZIC3"        "LHFPL4"      "ARSL"        "FAM81A"     
## [457] "PWWP3B"      "AFAP1L1"     "SNX22"       "COLEC12"     "RNF207"      "SHROOM4"    
## [463] "H2BC5"       "CD1C"        "NBL1"        "ADAMTS4"     "MPZ"         "TNNI1"      
## [469] "RUNX1"       "SIM2"        "SPON2"       "ZDHHC12"     "CHRNB2"      "PTH1R"      
## [475] "AZGP1"       "COL26A1"     "TAMALIN"     "ADCY9"       "SHANK2"      "LRP5"       
## [481] "FBLIM1"      "MXRA8"       "ADGRL4"      "LHX8"        "BRINP3"      "SLC9C2"     
## [487] "PKDCC"       "TRIM17"      "FRZB"        "ACTG2"       "EN1"         "MSX1"       
## [493] "C1QTNF7"     "NPPC"        "PBXIP1"      "FSTL1"       "IGFBP7"      "FEV"        
## [499] "IFI16"       "PRICKLE2"    "TIPARP"      "GYG1"        "GRIK3"       "CAMK2N2"    
## [505] "HEYL"        "BDH2"        "SPRY1"       "HSPA4L"      "GRM2"        "DUSP7"      
## [511] "PITX2"       "ADGRV1"      "F2RL1"       "SHROOM1"     "TMEM200A"    "SLC29A4"    
## [517] "COL1A2"      "SLC13A4"     "NOS3"        "FREM1"       "NIPSNAP3B"   "C9orf64"    
## [523] "CRYL1"       "VSTM4"       "FRMD7"       "NDRG2"       "C10orf82"    "ARHGAP42"   
## [529] "AMOTL1"      "GABRB3"      "PCBD1"       "CLMP"        "PPFIBP2"     "WDR72"      
## [535] "GALR1"       "ZCCHC18"     "STAT6"       "SAMD14"      "PRRX2"       "IGF2"       
## [541] "CACNB3"      "TTYH1"       "CDC42EP5"    "TMEM145"     "DNAAF3"      "KIFC2"      
## [547] "ANGPTL4"     "SOST"        "CASKIN1"     "ABCA3"       "MAP4K2"      "VASN"       
## [553] "FILIP1L"     "TAP1"        "HR"          "BMP1"        "GDNF"        "SLC16A4"    
## [559] "ABHD15"      "ATOH8"       "SLC35G2"     "STXBP6"      "PXDC1"       "ROR2"       
## [565] "AFAP1L2"     "SH3TC2"      "BNC1"        "TACR3"       "ROBO1"       "IFFO2"      
## [571] "MYRIP"       "NIPA1"       "SP7"         "SGCD"        "CAVIN4"      "GPR27"      
## [577] "CYTL1"       "HAS2"        "S1PR1"       "CDC42BPG"    "TMEM37"      "ZNF561"     
## [583] "PLEKHG5"     "VAT1L"       "LRRC34"      "COL8A2"      "PWWP2B"      "MLLT3"      
## [589] "AQP4"        "SCG2"        "SYNPO"       "SERF1A"      "ISG20"       "STARD5"     
## [595] "IL16"        "SYNPO2"      "CES3"        "MIR4435-2HG" "GXYLT2"      "BNC2"       
## [601] "SLC2A14"     "INSM1"       "PPP1R14B"    "CSPG4"       "ADGRG2"      "WFIKKN2"    
## [607] "GPR160"      "SPTBN2"      "C1QTNF1"     "CMKLR1"      "CD248"       "SEZ6L2"     
## [613] "CTBP2"       "PHYHD1"      "PCSK1"       "DENND2C"     "FOXG1"       "ZSCAN2"     
## [619] "PLAAT3"      "PHLDB3"      "NCKAP5"      "SCN4B"       "RIMKLA"      "FZD8"       
## [625] "LINC02904"   "HIC1"        "ZNF491"      "NECTIN3"     "ZNF354C"     "MAMDC4"     
## [631] "PARD6G"      "P4HTM"       "CA8"         "ERFE"        "RFLNA"       "CDH4"       
## [637] "WSCD1"       "MKRN3"       "H2AC6"       "MAP6D1"      "OXTR"        "PENK"       
## [643] "MAB21L2"     "GPR3"        "ZNF804B"     "BGN"         "LHFPL1"      "TCEAL7"     
## [649] "TMEM119"     "CCBE1"       "RIPK4"       "TENT5C"      "RFLNB"       "LHFPL6"     
## [655] "FOXL2"       "OLFML1"      "KIRREL1"     "ARSI"        "LRRC55"      "ST6GALNAC3" 
## [661] "ADRA2C"      "OLIG1"       "PRKD1"       "FOXO4"       "SLITRK6"     "B3GALT5-AS1"
## [667] "MANEAL"      "FAM43A"      "NOTUM"       "RBM11"       "PRKN"        "METTL7A"    
## [673] "ROR1"        "NR2F2"       "INKA1"       "SHC4"        "PMEL"        "LINC00839"  
## [679] "AGBL4"       "BCL9L"       "EDARADD"     "GOLGA8R"     "ZNF396"      "FOXD2"      
## [685] "PRR5"        "CYP27C1"     "MITF"        "SLIT1"       "FOXD3"       "GJA4"       
## [691] "PEAR1"       "PALM3"       "MAPK12"      "HEPACAM2"    "NUTM2B"      "INSC"       
## [697] "COL25A1"     "FAM83G"      "NKAIN2"      "SPRED3"      "APOD"        "IL1RAPL2"   
## [703] "BTBD8"       "SPOCK3"      "TDRD7"       "SERPINA3"    "KIF19"       "RYR1"       
## [709] "GRM7"        "ZNF124"      "ESRRG"       "MME"         "TLE1"        "H2AC11"     
## [715] "SERTAD1"     "FAM110D"     "KANK2"       "SVIL"        "UAP1L1"      "COL13A1"    
## [721] "FAM114A1"    "S100A10"     "IRAK4"       "LPAR1"       "NTRK1"       "MT1F"       
## [727] "ZNF480"      "TGM2"        "MIR29B2CHG"  "RBM20"       "RIPPLY2"     "BMPR2"      
## [733] "TCEA3"       "HLA-DOA"     "TAP2"        "MICA"        "DISP3"       "TBC1D8"     
## [739] "PCDHA9"      "LGR4"        "VIT"         "EIF3CL"      "LINC01597"   "ONECUT3"    
## [745] "NYNRIN"      "DOK6"        "FOXL2NB"     "CRIP1"       "GPC2"        "GPSM3"      
## [751] "KCTD11"      "ITGA1"       "MEF2B"       "ANXA2R-AS1"  "TNFRSF25"    "PPP1R3G"    
## [757] "CYTOR"       "CKMT1A"      "LINC02593"   "SNHG14"      "LMX1B-DT"    "PRRT4"      
## [763] "LINC01918"   "C14orf132"   "ZNF717"      "D21S2088E"   "LINC00858"   "PRAC2"      
## [769] "KHDC1-AS1"   "TFAP2A-AS1"  "HOXB-AS1"    "DNM3OS"      "FOXD3-AS1"   "LINC-PINT"  
## [775] "LINC00865"   "AJM1"        "HOTAIRM1"    "TWIST2"      "C12orf75"    "L3MBTL2-AS1"
## [781] "ARHGEF7-AS2" "CKMT1B"      "PRSS56"      "WAKMAR2"     "L1TD1"       "AQP1"       
## [787] "PNMA2"       "CD302"       "GLYCTK-AS1"  "EFNA4"       "TMEM35B"     "DBNDD2"     
## [793] "H2AJ"        "KCTD13-DT"   "APELA"       "GDNF-AS1"    "FMN1"        "PCDHA11"    
## [799] "TMEM150C"    "LINC01234"   "CARMN"       "CACNA1G-AS1" "LINC02762"   "SELENOP"    
## [805] "SNHG18"      "LRRC24"      "MAGEL2"      "B3GAT1-DT"   "TRIL"        "LINC01152"  
## [811] "LINC01956"   "FOXN3-AS1"   "FRRS1L"      "CDH3-AS1"    "CLEC19A"     "ISY1-RAB43" 
## [817] "MIA"         "LINC00621"   "LINC00672"   "GDF10"       "ZNF561-AS1"  "S1PR2"      
## [823] "BSG-AS1"     "MZF1-AS1"    "SLC25A53"    "CD24"        "LINC02538"   "MAP3K4-AS1" 
## [829] "TRABD-AS1"   "NATD1"       "RAB7B"       "PKD1L3"      "NKILA"       "PTENP1-AS"  
## [835] "EXOC3L2"    
## D50_AR 
##   [1] "SLC7A2"        "MAP3K9"        "TFAP2B"        "MGST1"         "GABRA3"       
##   [6] "SLC7A14"       "POLA2"         "CNTN1"         "PTPRN"         "DGKA"         
##  [11] "MPPED2"        "NAV3"          "SPTB"          "JMJD6"         "WIPI1"        
##  [16] "FOSL2"         "ACTL6B"        "MID2"          "B4GALT1"       "PPP1R13B"     
##  [21] "LHX5"          "ITGA6"         "RAPGEF4"       "MYO15A"        "HAUS4"        
##  [26] "TBC1D2"        "SYDE2"         "GCAT"          "HMOX1"         "SLC8A3"       
##  [31] "RSPO4"         "PAK5"          "PXMP4"         "SYNDIG1"       "CELF4"        
##  [36] "LAMA1"         "GLRA2"         "PCSK1N"        "NALCN"         "FGF14"        
##  [41] "NDRG4"         "SMPD3"         "COTL1"         "NDRG1"         "TUBB4A"       
##  [46] "LSR"           "SLC1A1"        "APBA1"         "CPEB3"         "NEURL1"       
##  [51] "SLC9A3R1"      "ZBTB16"        "JHY"           "TMEM109"       "MDK"          
##  [56] "TIMELESS"      "PRDM13"        "VEGFA"         "LOX"           "IRX4"         
##  [61] "PDE4D"         "FGF1"          "STC2"          "CBLB"          "SLC4A3"       
##  [66] "REEP6"         "EFHD1"         "ABCB6"         "ID3"           "PLPPR4"       
##  [71] "RCAN3"         "SLC8A2"        "TTR"           "SGIP1"         "PLAGL1"       
##  [76] "STBD1"         "ACOT2"         "PPP1R3C"       "MOB3B"         "GRIA2"        
##  [81] "ENOX1"         "SLITRK3"       "MYOG"          "PHF24"         "BHLHE41"      
##  [86] "OPTN"          "CPNE5"         "GRIA3"         "MCHR1"         "RNF112"       
##  [91] "FLNC"          "SYT5"          "LGALS3"        "SNAP25"        "ATP8A2"       
##  [96] "CHRM3"         "MYH8"          "DUSP26"        "BHLHE40"       "IAH1"         
## [101] "P2RX4"         "FAIM2"         "FHOD1"         "RAPGEF5"       "SCN2A"        
## [106] "RALGPS1"       "PRCP"          "GLCE"          "FBN2"          "RBP5"         
## [111] "PHLDA1"        "SDSL"          "SLC46A3"       "SYT16"         "CELF6"        
## [116] "LMTK3"         "IGLON5"        "FHAD1"         "SEMA6C"        "TMEFF2"       
## [121] "ABCA12"        "PHLDB2"        "TMEM108"       "AMT"           "TNFAIP8"      
## [126] "PRSS35"        "SLC2A12"       "GPC3"          "NR6A1"         "NCAM1"        
## [131] "HMGA2"         "DLG2"          "MFSD6"         "SERP2"         "GRIA4"        
## [136] "NRSN1"         "PTPRR"         "CACNA2D1"      "CABYR"         "SLA"          
## [141] "GPR61"         "KCNS2"         "SYN2"          "STC1"          "CLIC6"        
## [146] "CFAP157"       "SPTBN4"        "CELF5"         "PLXDC1"        "GRIN2C"       
## [151] "CYGB"          "TEDC2"         "B3GALT2"       "IER5"          "RFTN2"        
## [156] "VSNL1"         "INAVA"         "CADPS"         "PRSS12"        "NPY1R"        
## [161] "EDIL3"         "RNF180"        "GRIK2"         "STK17A"        "ADCY1"        
## [166] "CSMD3"         "CACNB2"        "SCN3B"         "TMEM130"       "C18orf54"     
## [171] "CACNG2"        "SCG5"          "PBX3"          "ATCAY"         "HID1"         
## [176] "GRM5"          "ZNF354A"       "TMEM266"       "FAM153A"       "IRX1"         
## [181] "KSR2"          "DLK2"          "CES4A"         "ARPP21"        "TTC9B"        
## [186] "SPSB4"         "CHST1"         "LINC01106"     "LRRTM4"        "MAMSTR"       
## [191] "EPS8L2"        "KCNA2"         "RPRM"          "PCDHB9"        "ADAMTSL1"     
## [196] "AMER3"         "SHISA3"        "TMTC2"         "TMEM151A"      "MROH1"        
## [201] "ZNF154"        "NRXN1"         "MYL11"         "LINC00304"     "UNC5C"        
## [206] "TSPEAR-AS2"    "SLC8A1"        "EFHC2"         "KCND2"         "CEND1"        
## [211] "RALYL"         "TCEAL2"        "ROBO2"         "PDIA2"         "SRL"          
## [216] "KCNIP4"        "IKZF1"         "IRS2"          "FAM228A"       "MIR22HG"      
## [221] "FSCN2"         "ESPN"          "LHFPL3"        "VWC2"          "SKOR1"        
## [226] "GREB1"         "ZNF836"        "AFAP1"         "H2BU1"         "LRRC8B"       
## [231] "COL4A6"        "DMBX1"         "DNM3"          "HMGN5"         "SLC29A3"      
## [236] "GRIN3A"        "RYR3"          "RASGEF1A"      "SOWAHA"        "ZNF525"       
## [241] "NHSL2"         "LINC02731"     "PCDHA5"        "LOH12CR2"      "TRIM71"       
## [246] "XKR4"          "CAPN14"        "ARHGEF28"      "BASP1-AS1"     "SKOR2"        
## [251] "SIAH3"         "GPC1-AS1"      "INO80D-AS2"    "NUTM2E"        "DIRC3"        
## [256] "STXBP5-AS1"    "ANKRD65"       "C2orf74"       "ARHGDIG"       "PCDHGC4"      
## [261] "LINC00461"     "HS3ST5"        "TMEM158"       "PCDH10-DT"     "LYN"          
## [266] "MIR100HG"      "LINC02293"     "LINC02883"     "SCX"           "STAM-DT"      
## [271] "XKR7"          "PCDHGA4"       "GABRQ"         "UNC5C-AS1"     "ZSWIM8-AS1"   
## [276] "PCDHB16"       "CSGALNACT2-DT" "INSIG1-DT"     "TMEM271"       "LINC02334"    
## [281] "SEPSECS-AS1"   "PEG13"         "LINC01902"     "DERPC"        
## D50_HT 
##    [1] "TNMD"       "STPG1"      "TMEM176A"   "PDK4"       "SLC25A13"   "MCUB"       "CROT"      
##    [8] "SOX8"       "ITGA2B"     "CACNG3"     "ALDH3B1"    "SCIN"       "PAX6"       "BAIAP3"    
##   [15] "E2F2"       "MLXIPL"     "CD9"        "NCAPD2"     "LRRC23"     "SYT7"       "ANLN"      
##   [22] "BRCA1"      "EHD3"       "TACC3"      "STMN4"      "PLEKHB1"    "GRAMD1B"    "DEPDC1"    
##   [29] "TYMP"       "VRK2"       "ARHGAP31"   "DEPDC1B"    "TNC"        "PREX2"      "ANO2"      
##   [36] "NEDD4L"     "RAD51"      "POLQ"       "MSMO1"      "NRIP2"      "ENTPD2"     "OPN3"      
##   [43] "HHAT"       "GYG2"       "F7"         "RASGRF1"    "YBX3"       "MPC1"       "EYA2"      
##   [50] "CNN2"       "ABCA7"      "HMG20B"     "MCM10"      "PACC1"      "TLE2"       "NGEF"      
##   [57] "ASPM"       "KIF26A"     "PFKP"       "PHKA1"      "COASY"      "ACSL4"      "PRR11"     
##   [64] "PTPN3"      "CHAT"       "TRIP13"     "HMMR"       "EVC"        "NDE1"       "IRAG1"     
##   [71] "MCM2"       "GSDMB"      "GLI2"       "TEAD2"      "CA12"       "ENO1"       "SEMA3A"    
##   [78] "GTSE1"      "CACNG5"     "WDR62"      "ARHGAP15"   "FMO4"       "RGS11"      "SPAG5"     
##   [85] "TPD52"      "ACACB"      "GPC4"       "MBNL3"      "STXBP2"     "NAALAD2"    "SLC25A43"  
##   [92] "NEBL"       "RBFOX1"     "SLC1A3"     "LXN"        "FDFT1"      "OPHN1"      "EPB41L2"   
##   [99] "EPHA6"      "SLC4A4"     "CHRNA3"     "KCNN2"      "NDC80"      "TCF7"       "CDH7"      
##  [106] "ARG2"       "STK17B"     "PGR"        "TRAF5"      "PLOD1"      "KIF3C"      "MECOM"     
##  [113] "OVGP1"      "ORC1"       "RAD54L"     "MAST2"      "EPDR1"      "HBQ1"       "MT3"       
##  [120] "AURKA"      "GP6"        "TPX2"       "CPXM1"      "TESC"       "FUS"        "BIRC5"     
##  [127] "LAG3"       "YPEL3"      "IRAK3"      "KIF4A"      "DLL3"       "ABCC6"      "NLRP1"     
##  [134] "ZFHX4"      "RGS17"      "SLC7A8"     "SEMA6A"     "CLSPN"      "TGFB2"      "CDC45"     
##  [141] "ADA2"       "XYLB"       "CDC6"       "EPB41L4B"   "SH2D3C"     "CRTAC1"     "PCDH11Y"   
##  [148] "HNRNPM"     "SLC7A4"     "SEZ6L"      "CENPM"      "SEPTIN3"    "SLC5A4"     "MCM5"      
##  [155] "TSPO"       "RASD2"      "APOL4"      "PNPLA3"     "KHNYN"      "COCH"       "POLE2"     
##  [162] "PYGL"       "CCDC198"    "PAPLN"      "NFATC4"     "VSX1"       "MYBL2"      "PABPC1L"   
##  [169] "HRH3"       "TRIB3"      "E2F1"       "AHCY"       "FAM83D"     "ST8SIA5"    "PRPS2"     
##  [176] "CHRDL1"     "ZC3H12B"    "KLF8"       "SRPX2"      "OLFM4"      "CORO1A"     "HAS3"      
##  [183] "NECAB2"     "NME4"       "SLC7A5"     "EEF2K"      "SYT17"      "CORO2B"     "ACSBG1"    
##  [190] "IGDCC4"     "FAM189A1"   "OIP5"       "EYA1"       "STK3"       "PYCR3"      "ARHGEF10"  
##  [197] "MCM4"       "IL27RA"     "ASF1B"      "SYDE1"      "AURKC"      "CCNE1"      "PRX"       
##  [204] "MYH14"      "LIG1"       "TMEM59L"    "ZC3HAV1"    "CAV2"       "HOXA2"      "VIPR2"     
##  [211] "EVX1"       "CPVL"       "MINDY4"     "NPTX2"      "TMEM176B"   "GLI3"       "TLE4"      
##  [218] "SUSD1"      "AKNA"       "RLN2"       "KCNT1"      "DDX58"      "GLIS3"      "PDLIM1"    
##  [225] "CDH23"      "SPOCK2"     "SH3PXD2A"   "SYNGR2"     "LGALS3BP"   "DHX58"      "PHOX2B"    
##  [232] "NFKB1"      "NCAPG"      "PPARGC1A"   "CTSC"       "CCDC34"     "B3GAT1"     "UNC93B1"   
##  [239] "NECTIN1"    "PTPMT1"     "SYT10"      "LIN7A"      "GLI1"       "FOXM1"      "PRMT8"     
##  [246] "RAD51AP1"   "MGP"        "SLC38A1"    "TBC1D30"    "GAPDH"      "CDCA3"      "NEDD9"     
##  [253] "MCM9"       "RIPOR2"     "FBXO5"      "SRSF3"      "MCM3"       "GLP1R"      "BMP5"      
##  [260] "E2F3"       "BVES"       "COL9A1"     "B3GAT2"     "PACRG"      "PDE10A"     "TTK"       
##  [267] "HMGCS1"     "KIF20A"     "TMCO6"      "PCDHB6"     "CCNG1"      "SLC12A7"    "GNPDA1"    
##  [274] "LIFR"       "CPEB4"      "HRH2"       "SMC4"       "BCHE"       "ECT2"       "GBE1"      
##  [281] "RTKN"       "KCNIP3"     "TP53I3"     "GPD2"       "CENPA"      "SLC30A3"    "LOXL3"     
##  [288] "ACADL"      "DNAH6"      "TPO"        "ID2"        "SLC1A4"     "ATP6V1B1"   "PAPPA2"    
##  [295] "ERRFI1"     "HDAC1"      "LEPR"       "PLA2G4A"    "RPE65"      "TTF2"       "BMP8B"     
##  [302] "ST6GALNAC5" "IGSF21"     "KIF17"      "RAB29"      "CDC20"      "TSPAN1"     "F3"        
##  [309] "NEK2"       "CENPF"      "KIF14"      "FILIP1"     "PMFBP1"     "SLC16A7"    "ARMC2"     
##  [316] "TGIF2"      "PCDH17"     "ELL2"       "PHF19"      "IRF2BPL"    "LTBP2"      "PPP4R4"    
##  [323] "TGFB3"      "ESRRB"      "GPR75"      "HELLS"      "KCNIP2"     "ARAP3"      "TNN"       
##  [330] "CENPL"      "MASTL"      "SMAD9"      "DUSP4"      "ADRA1A"     "EPHX2"      "SCPEP1"    
##  [337] "FAM117A"    "NCAPH"      "ADCY7"      "TSHZ3"      "KCNJ8"      "A1BG"       "KIF18A"    
##  [344] "FABP3"      "CPXM2"      "TMEM54"     "ANXA11"     "PTGFR"      "HOXA7"      "CHST3"     
##  [351] "ZWINT"      "CDKN2C"     "CENPK"      "NCKAP1L"    "CDK2"       "STIL"       "HJURP"     
##  [358] "CKS2"       "SLC12A4"    "SDC4"       "CHST8"      "IQSEC2"     "SERPINB6"   "AHNAK"     
##  [365] "DOK4"       "CLYBL"      "ABCC4"      "HROB"       "BARHL1"     "PAX8"       "CD70"      
##  [372] "FAM182A"    "PAX1"       "GDF5"       "NECAB3"     "ID1"        "XRCC3"      "THRA"      
##  [379] "DLGAP5"     "FGD3"       "AUNIP"      "KLF2"       "PKMYT1"     "WFIKKN1"    "METTL25"   
##  [386] "YWHAH-AS1"  "SPECC1"     "MYO1B"      "MYO5C"      "TMOD2"      "DLL4"       "CLN6"      
##  [393] "TPH1"       "DCTD"       "PIMREG"     "PLD2"       "PUS7L"      "AJUBA"      "MIS18BP1"  
##  [400] "CDO1"       "SGO1"       "SAT1"       "KIF1A"      "ARPC1B"     "PGPEP1"     "HRC"       
##  [407] "OLFM1"      "HELZ2"      "CALY"       "FIBCD1"     "THEMIS2"    "SLC35D2"    "C1QL1"     
##  [414] "RFTN1"      "AOC3"       "AOC2"       "IL13RA1"    "TOP2A"      "ZNF132"     "PODNL1"    
##  [421] "DNAJB1"     "ENOSF1"     "PTPRE"      "COQ3"       "TRIM47"     "PCBD2"      "PCNA"      
##  [428] "ATP1A4"     "NES"        "TOE1"       "LPIN3"      "VSTM2L"     "PATJ"       "CCNA1"     
##  [435] "TRPC4"      "RFC3"       "AMPD3"      "TEX15"      "TTC9"       "CCNB1"      "VAV3"      
##  [442] "PSRC1"      "TRIM45"     "MYCN"       "ANO3"       "FST"        "ECHDC3"     "CDCA8"     
##  [449] "DSC2"       "DTNA"       "CEMIP2"     "HRK"        "TMEM243"    "CD36"       "HTR1B"     
##  [456] "EPHA7"      "PRPH"       "GLS2"       "TROAP"      "ESPL1"      "HNRNPA1"    "FBXL8"     
##  [463] "CCDC102A"   "RGS8"       "RNASEL"     "USP44"      "SLC41A2"    "PCDH8"      "RNASEH2B"  
##  [470] "CKAP2"      "BORA"       "MYCBPAP"    "BRIP1"      "GYPC"       "SMC2"       "KLF4"      
##  [477] "TMOD1"      "DSCC1"      "CCN3"       "TCF19"      "IER3"       "ATAT1"      "MYO7A"     
##  [484] "SYTL2"      "RAB30"      "DDX60"      "ARHGAP20"   "NUSAP1"     "KIF23"      "KNL1"      
##  [491] "UACA"       "TMEM62"     "FNBP1L"     "ARHGAP29"   "CENPO"      "MYOF"       "KIF11"     
##  [498] "DUSP5"      "CEP55"      "KIF20B"     "ENTPD1"     "PLCE1"      "BARD1"      "SLC40A1"   
##  [505] "PPCDC"      "FAM13A"     "BMPR1B"     "PRDM5"      "FRAS1"      "SHROOM3"    "CENPE"     
##  [512] "SLC39A8"    "SHISAL1"    "TMEM117"    "GLIPR1"     "DUSP6"      "GAS2L3"     "RDH16"     
##  [519] "BRCA2"      "ESYT1"      "VPS37B"     "RHOF"       "DIAPH3"     "CBLN3"      "MDGA2"     
##  [526] "DUOXA1"     "PSTPIP1"    "PIF1"       "FANCI"      "TICRR"      "TGFB1I1"    "MARVELD3"  
##  [533] "ADAMTS18"   "CDH13"      "KSR1"       "TOM1L1"     "ADCYAP1"    "NFIC"       "IFITM3"    
##  [540] "HUNK"       "APP"        "CACNG8"     "EPHA2"      "CNKSR1"     "C1orf216"   "C1orf94"   
##  [547] "PLK4"       "MAP3K6"     "KIF2C"      "MOB3C"      "BARHL2"     "C1orf162"   "NUF2"      
##  [554] "CASQ1"      "RGS16"      "LHX9"       "SELENBP1"   "OAZ3"       "GABPB2"     "DTL"       
##  [561] "DYRK3"      "SLC27A3"    "GDF7"       "CHAC2"      "ABHD1"      "FBLN7"      "AFF3"      
##  [568] "NXPH2"      "SUMF1"      "ACKR3"      "FANCD2"     "CTDSP1"     "GRIP2"      "IL17RD"    
##  [575] "IGSF11"     "NR1I2"      "BOC"        "DGKQ"       "SCD5"       "TIFA"       "CCNA2"     
##  [582] "USP53"      "PDGFC"      "PIK3R1"     "LIX1"       "ZNF300"     "GFOD1"      "TRIM7"     
##  [589] "TNFRSF21"   "RASGEF1C"   "SCUBE3"     "GABRR1"     "ABRACL"     "MTFR2"      "TIAM2"     
##  [596] "CREB5"      "CDCA5"      "TMEM168"    "NCAPG2"     "SH3KBP1"    "MSN"        "CHST7"     
##  [603] "LPAR4"      "GINS4"      "CRH"        "PMP2"       "ATP6V0D2"   "PLIN2"      "CDKN2A"    
##  [610] "IDNK"       "SHC3"       "GSN"        "ST8SIA6"    "RGR"        "MKI67"      "FUOM"      
##  [617] "GSTO1"      "SERPING1"   "RPS3"       "TTC12"      "GLB1L2"     "GRIK4"      "INCENP"    
##  [624] "CHEK1"      "KIRREL3"    "DSN1"       "ALDOA"      "FAM124A"    "PRSS23"     "DOCK1"     
##  [631] "PIH1D2"     "KCNA6"      "MAT1A"      "TEX30"      "ME3"        "ANO4"       "POU4F2"    
##  [638] "NR3C2"      "INPP1"      "CENPU"      "CCDC122"    "ZNF385D"    "SLC35F4"    "PARP8"     
##  [645] "MGAT5"      "PSTPIP2"    "SPC25"      "HOMER1"     "ZSCAN1"     "SPARCL1"    "RASGRP3"   
##  [652] "ZIC1"       "CENPH"      "SYCP2L"     "BMP6"       "LPCAT1"     "C16orf89"   "CMTM7"     
##  [659] "CD8A"       "KCNJ16"     "DDAH1"      "ANKFN1"     "THY1"       "JPH3"       "UCHL1"     
##  [666] "TNIK"       "PGM5"       "TMPRSS15"   "NCAM2"      "JAM2"       "ADAMTS5"    "SKA1"      
##  [673] "APCDD1"     "PIEZO2"     "USP43"      "RAB6B"      "EME1"       "ACSS1"      "ADCY8"     
##  [680] "CFAP70"     "KCNMA1"     "SFXN2"      "FUT6"       "FBXO43"     "HKDC1"      "MAPK13"    
##  [687] "ATAD2"      "FRRS1"      "BUB1B"      "SST"        "NMNAT2"     "ATP2B2"     "NRG1"      
##  [694] "STEAP2"     "FZD1"       "CACNA1D"    "CCNB2"      "ETS2"       "DRC1"       "MEGF11"    
##  [701] "SLC30A2"    "UBXN11"     "GALNT14"    "DZIP1L"     "CDC25C"     "H4C8"       "GDPD5"     
##  [708] "SLC45A3"    "F11R"       "CCDC24"     "IGF2BP1"    "CBR1"       "HK2"        "CELF3"     
##  [715] "THEM4"      "TCHH"       "NPR2"       "ZNF233"     "TNFRSF13C"  "ABCG1"      "PDE9A"     
##  [722] "C21orf58"   "ZNF761"     "PKN3"       "RUSC1"      "NBEAL2"     "RECQL4"     "LRRC56"    
##  [729] "ITGA5"      "ZNF385A"    "PLCD3"      "SPC24"      "CCNF"       "LBHD1"      "PDPN"      
##  [736] "CAMK2N1"    "WNT4"       "SNX7"       "NTNG1"      "AKNAD1"     "ATXN7L2"    "CADM3"     
##  [743] "KCNJ9"      "PEA15"      "OLFML2B"    "ACP6"       "KCNF1"      "KCNJ3"      "ARHGAP25"  
##  [750] "FZD5"       "SLC15A2"    "LMOD1"      "ADORA1"     "CIP2A"      "SGO2"       "SERPINI1"  
##  [757] "NUAK2"      "RPL22L1"    "PTPN13"     "C4orf36"    "PPM1K"      "KIF15"      "FYCO1"     
##  [764] "KLF15"      "ABLIM2"     "CDC25A"     "POC1A"      "ETNPPL"     "MAD2L1"     "SMIM43"    
##  [771] "NPY5R"      "HHIP"       "ZNF474"     "FABP7"      "TLX3"       "HCN1"       "NEUROD6"   
##  [778] "PTTG1"      "CDCA7L"     "SP8"        "HEY1"       "FABP5"      "HNF4G"      "EN2"       
##  [785] "NFIL3"      "FXN"        "PCDH19"     "WNK2"       "MELK"       "HECTD2"     "SKA3"      
##  [792] "DDIAS"      "LRR1"       "ZNF22-AS1"  "TMEM63C"    "NGB"        "AKR1E2"     "DRGX"      
##  [799] "HTRA1"      "PLEKHF1"    "NUDT13"     "LMO1"       "CENPN"      "WEE1"       "PRKCB"     
##  [806] "CPLX4"      "CFAP52"     "TVP23A"     "SLFN5"      "PCLAF"      "LDHD"       "RBPMS2"    
##  [813] "PLK1"       "NEMP1"      "STX3"       "MTMR10"     "MS4A8"      "MAPRE2"     "NAT16"     
##  [820] "SGSM1"      "ACSF2"      "ART5"       "MVD"        "CDT1"       "AXL"        "PPP1R14A"  
##  [827] "CHAF1A"     "TRPV3"      "TK1"        "ATG16L2"    "CCDC88B"    "PBK"        "PNOC"      
##  [834] "GLYCTK"     "IRF2BP2"    "SCN11A"     "MFSD2A"     "TNXB"       "LGI3"       "PHYHIP"    
##  [841] "GSTM4"      "SHOX2"      "ENHO"       "LGALS9"     "RGS14"      "CKAP2L"     "HIC2"      
##  [848] "BUB1"       "AGPAT2"     "LDB2"       "P2RY1"      "WNT10B"     "FRMPD4"     "TMEM42"    
##  [855] "GPR37L1"    "CMTM8"      "CDK1"       "FOS"        "SLC30A1"    "MGMT"       "TRABD"     
##  [862] "ZNF296"     "CDCA4"      "MTSS1"      "JUNB"       "SHCBP1"     "ESCO2"      "LURAP1"    
##  [869] "COL24A1"    "NEUROD2"    "CXXC5"      "BCL2"       "RRM2"       "SRGAP2C"    "MAL"       
##  [876] "MBOAT1"     "CEBPB"      "CSDC2"      "RCAN2"      "PRSS27"     "RSPH9"      "FUT9"      
##  [883] "SMPDL3A"    "EFEMP2"     "THEMIS"     "CYP7B1"     "METAP1D"    "LVRN"       "SH3RF3"    
##  [890] "HSPA6"      "ADAMTS20"   "GLRX"       "SYT12"      "PPP1R3B"    "TRIB1"      "CEP83"     
##  [897] "SCAI"       "SUSD5"      "PLK3"       "MARCHF3"    "TCAP"       "TLR1"       "NWD2"      
##  [904] "EVX2"       "EXO1"       "CRMA"       "ZCCHC12"    "TMEM81"     "KY"         "FGFBP3"    
##  [911] "AMZ1"       "ZIC4"       "UBE2C"      "TRAF6"      "FAM182B"    "CSRP2"      "VWA3A"     
##  [918] "CCNE2"      "MCTP1"      "TSGA10IP"   "SUGCT"      "RMI2"       "PRIMA1"     "ETV4"      
##  [925] "HOXD8"      "SPHK1"      "ACBD7"      "DMRTA1"     "DNAJC30"    "CLK2"       "LPCAT4"    
##  [932] "KBTBD11"    "ZNF843"     "IRX5"       "TYMS"       "PXMP2"      "TYMSOS"     "SIX5"      
##  [939] "ACER2"      "CLVS1"      "HASPIN"     "FAM20C"     "ODF3B"      "DPY19L2"    "PDE4DIP"   
##  [946] "ZNF114"     "SH2D4B"     "GEN1"       "AQP11"      "NEUROG2"    "MAF"        "ZNF713"    
##  [953] "RPP25"      "CPNE7"      "EFCAB13"    "APOLD1"     "PFAS"       "HES7"       "VWA1"      
##  [960] "FJX1"       "ZBTB42"     "RPRML"      "ANKRD18A"   "LYNX1"      "TH"         "RCC1"      
##  [967] "PLD5"       "ALX1"       "GAS1"       "GSX2"       "SSTR2"      "ZNF594"     "MAB21L1"   
##  [974] "GPR157"     "FANCB"      "C6orf223"   "TIGIT"      "RTKN2"      "TRIM49B"    "FAM181B"   
##  [981] "CREB3L2"    "KCNA4"      "NXPH4"      "KPNA2"      "NTM"        "KCNB2"      "IGIP"      
##  [988] "RGS6"       "PAPPA"      "GRID1"      "GALNT9"     "ADGRG3"     "CADM1"      "SLC25A21"  
##  [995] "SLC25A10"   "BEGAIN"     "FAM43B"     "CSMD1"      "C2CD4C"     "POTEC"     
##  [ reached getOption("max.print") -- omitted 357 entries ]

D25_AR:D50_AR

all_intersections$`D25_AR:D50_AR`
##  [1] "FZD10"     "TFCP2"     "SLC15A4"   "TPPP3"     "PFKFB3"    "H2AW"      "BCAM"     
##  [8] "ZNF605"    "ZNF100"    "PCDHA4"    "PCDHA13"   "FZD10-AS1" "LHX1"      "LHX1-DT"

D25_AR:D50_HT

all_intersections$`D25_AR:D50_HT`
## [1] "DSG2"    "GPR50"   "CLU"     "LMO2"    "GRIA1"   "PPP1R32" "SERINC5" "CRABP1"

D25_HT:D25_AR

all_intersections$`D25_HT:D25_AR`
##  [1] "BMP7"           "BMF"            "DNAI1"          "SSUH2"          "MNS1"          
##  [6] "LEF1"           "HDC"            "MYBPC1"         "BLOC1S5-TXNDC5" "TXNIP"

D25_HT:D50_AR

all_intersections$`D25_HT:D50_AR`
##  [1] "RUNX1T1"      "SORBS1"       "EEF1A2"       "PCYT1B"       "SEMA5A"       "CDH9"        
##  [7] "RBP1"         "FNDC4"        "BCL11A"       "NXPH1"        "MMP24"        "NOTCH2"      
## [13] "STK26"        "TNS3"         "ARHGAP24"     "AMIGO2"       "COL2A1"       "DISP2"       
## [19] "CCDC33"       "KIFC3"        "GAS8"         "CRABP2"       "HMGCLL1"      "GRM1"        
## [25] "ANKRD29"      "ROBO3"        "ADAMTS1"      "VCAM1"        "UNCX"         "EFNA1"       
## [31] "DSCAM"        "NEGR1"        "SLITRK1"      "BACE2"        "OAF"          "HS6ST3"      
## [37] "CPNE4"        "LRRTM3"       "C2orf72"      "ARHGEF35-AS1"

D25_HT:D50_HT

all_intersections$`D25_HT:D50_HT`
##   [1] "HS3ST1"      "KLHL13"      "SKAP2"       "GCFC2"       "CRLF1"       "TMEM132A"   
##   [7] "DNAH9"       "GAS7"        "TKTL1"       "CAMK1G"      "NFIX"        "TENM1"      
##  [13] "MTMR11"      "ATP1A2"      "ZNF582"      "CD74"        "ADGRA2"      "FAS"        
##  [19] "TMSB10"      "COL9A2"      "FOXC1"       "PARP12"      "PRDM6"       "NGFR"       
##  [25] "ME1"         "TGFBR3"      "FGF10"       "NCK2"        "SPEG"        "ST6GAL1"    
##  [31] "ZNF37A"      "PAX2"        "MCAM"        "ADCY2"       "SESN1"       "LYRM2"      
##  [37] "EFR3B"       "PPEF1"       "BAX"         "ADAMTS2"     "GNAO1"       "SLC4A11"    
##  [43] "LAMB1"       "WDR76"       "COL9A3"      "COMT"        "CYP26A1"     "MFNG"       
##  [49] "LGALS1"      "SOX10"       "TIMP3"       "RIN3"        "DHRS2"       "SLCO4A1"    
##  [55] "RNF125"      "TIMP1"       "SYTL4"       "FGF9"        "DGKH"        "MAPK3"      
##  [61] "GDPD3"       "TRPA1"       "SLC1A6"      "TFPI2"       "LHX2"        "ENG"        
##  [67] "SH3GL2"      "RASSF4"      "TLX1"        "SFXN3"       "PNPO"        "SOX6"       
##  [73] "TNS2"        "ELK3"        "OAS3"        "MDGA1"       "KHDRBS2"     "ASCC3"      
##  [79] "PCDHB5"      "CDH6"        "PDGFRB"      "UNC5A"       "EHHADH"      "MRPL3"      
##  [85] "POMC"        "ITGA4"       "HPCAL1"      "QPCT"        "DLX2"        "PRRX1"      
##  [91] "KIF21B"      "ZNHIT6"      "SLC2A1"      "NENF"        "PROX1"       "NRP2"       
##  [97] "RAB32"       "ONECUT2"     "PYROXD2"     "ACAT2"       "KIAA1217"    "EGR1"       
## [103] "TNFRSF10B"   "CAT"         "ARL4A"       "GLIPR2"      "PLP1"        "CDKN1A"     
## [109] "MT2A"        "TNFSF9"      "CITED1"      "FLRT1"       "PLEKHG3"     "TMEM35A"    
## [115] "LRRC61"      "GNG11"       "RASL11B"     "LIF"         "DOCK4"       "FEZF1"      
## [121] "ISLR"        "LOXL1"       "E2F8"        "SOX15"       "CD68"        "MTUS1"      
## [127] "RPS4Y1"      "GAMT"        "GDPD2"       "SH3BP4"      "COL5A1"      "MED18"      
## [133] "HIP1R"       "PNCK"        "DUSP9"       "EDA2R"       "RAB11FIP4"   "SLC6A6"     
## [139] "GFPT2"       "SLC6A11"     "NUP210"      "RAP1GAP2"    "BCAN"        "PPP1R3D"    
## [145] "DCLK1"       "POSTN"       "STARD13"     "NTS"         "SWAP70"      "RNF122"     
## [151] "CAMK1"       "SYT6"        "CMPK2"       "DAGLA"       "ADAM19"      "BICDL1"     
## [157] "MDM2"        "SP110"       "SERPINE2"    "DRAM1"       "GPNMB"       "GAD2"       
## [163] "CTSV"        "MYC"         "TFAP2A"      "FOXF2"       "SLCO5A1"     "ITGA11"     
## [169] "ZNF280D"     "IFI44L"      "IFI44"       "SIX3"        "ZNF365"      "STAT4"      
## [175] "HECW2"       "PARP9"       "SEMA7A"      "HERC5"       "CPNE8"       "FOXN4"      
## [181] "GRTP1"       "ARMH4"       "NEIL1"       "ST8SIA2"     "TIGD7"       "MAPK4"      
## [187] "STAC2"       "PLPP2"       "PGGHG"       "HMCN1"       "CGN"         "EFNA3"      
## [193] "CNGA3"       "SLC4A10"     "DLX1"        "SPAG16"      "ITGA9"       "IGFBP3"     
## [199] "DIAPH2"      "RGS20"       "STOM"        "LCN9"        "PROSER2"     "PAOX"       
## [205] "RGS10"       "CDH8"        "GPM6A"       "FREM2"       "TMEM86A"     "ABTB3"      
## [211] "GFRA1"       "TRIM36"      "PLEKHH2"     "ZNF117"      "RASSF3"      "NMRAL1"     
## [217] "LGI4"        "UBASH3B"     "PITPNC1"     "OBSCN"       "DKK2"        "PTPRN2"     
## [223] "AFF2"        "WIF1"        "MPV17L"      "MMP14"       "C2CD2"       "PSMG3"      
## [229] "XKR8"        "CLSTN2"      "SLC13A3"     "DMTN"        "S100B"       "LY6E"       
## [235] "FDXR"        "ZNF75A"      "AK4"         "NFIA"        "DDR2"        "SPATA18"    
## [241] "TAFA4"       "CDS1"        "PTX3"        "APBB2"       "DTX3L"       "PRKCD"      
## [247] "ARHGEF3"     "EXO5"        "ERMAP"       "ITGA2"       "F2RL2"       "CMBL"       
## [253] "EGFLAM"      "UBLCP1"      "ACSL6"       "DLC1"        "SPIDR"       "VEGFD"      
## [259] "PHOX2A"      "PKNOX2"      "E2F7"        "PACSIN3"     "KCNC2"       "ADAMTS15"   
## [265] "IKBIP"       "ALKBH3"      "TMEM100"     "CHRFAM7A"    "ELFN2"       "GREM1"      
## [271] "TUBA1C"      "ZNF528"      "PLIN4"       "RAB3IL1"     "SCARA3"      "MMADHC"     
## [277] "COL3A1"      "GFRA2"       "INPP5D"      "CHST14"      "PCSK9"       "KCNK9"      
## [283] "ONECUT1"     "GPRC5C"      "EMB"         "SIX2"        "DLGAP1"      "POLH"       
## [289] "PRKCE"       "NPTX1"       "CLCN5"       "DSEL"        "ZNF562"      "ECEL1"      
## [295] "GATM"        "CFAP46"      "PRNP"        "FRMD5"       "FRMD3"       "ZMAT3"      
## [301] "ZNF596"      "RARG"        "MYD88"       "ZNF680"      "PARP14"      "PTPRM"      
## [307] "VEGFB"       "TNFRSF10C"   "JUP"         "HAP1"        "CTSF"        "MSRB3"      
## [313] "PHLDA3"      "ZNF25"       "ALG10B"      "FOSL1"       "MTLN"        "TUBB6"      
## [319] "ZNF135"      "HSD11B2"     "RIMS2"       "RNF152"      "BDNF"        "BOK"        
## [325] "TCERG1L"     "TCIM"        "KCNA3"       "ANXA2R"      "ANXA2R-OT1"  "ZNF619"     
## [331] "ZNF454"      "POGLUT3"     "NRIP1"       "TSPYL5"      "ZFP3"        "ARSJ"       
## [337] "FAM83H"      "AEN"         "TMEM132E"    "TMIE"        "ZNF875"      "CHST15"     
## [343] "KCNIP1"      "PLCB1"       "RNF32-DT"    "SPNS2"       "CHST6"       "MAGEA2B"    
## [349] "CCDC125"     "BCOR"        "FHL3"        "TRIM61"      "ZNF703"      "ANKRD45"    
## [355] "CFAP91"      "PNMA3"       "ZNF730"      "TBX1"        "CNTN2"       "ALDH1A3"    
## [361] "CSF1"        "TXNRD2"      "LRRC26"      "SRY"         "TMEM121"     "RPS27L"     
## [367] "INPP5J"      "AHNAK2"      "OLFML2A"     "NDUFA4L2"    "PRAME"       "C11orf87"   
## [373] "IFIT1"       "RTN4RL1"     "SHOX"        "ZNF225-AS1"  "ANKRD37"     "ZNF501"     
## [379] "HPDL"        "PDZD7"       "WDR86"       "SAMD11"      "POTEE"       "PRELP"      
## [385] "SHISA6"      "H1-0"        "SP6"         "PLAC9"       "ZNF527"      "ZNF33A"     
## [391] "PAX8-AS1"    "FAM217B"     "ZNF107"      "NTNG2"       "ARL9"        "CACNA1H"    
## [397] "AJAP1"       "POTEF"       "ZNF502"      "POTEI"       "ARID5A"      "ZNF585A"    
## [403] "ZNF138"      "ZNF429"      "ZNF470"      "ADARB1"      "PDGFA"       "EME2"       
## [409] "H2BC12"      "HES5"        "ZNF71"       "ZNF560"      "ZNF273"      "ZNF248"     
## [415] "HOXC4"       "ZNF583"      "ZNF534"      "EIF1AY"      "INPP5F"      "CCDC152"    
## [421] "CSAG1"       "TCEAL5"      "HSPA1A"      "HLA-C"       "INSYN2B"     "PNMA8B"     
## [427] "LRRC10B"     "MUC19"       "C21orf62"    "GOLGA8O"     "HLA-A"       "GPX3"       
## [433] "MAGEA12"     "ERV3-1"      "EMP2"        "LTB4R"       "FAM66B"      "SCRT2"      
## [439] "HMX1"        "LINC01139"   "LINC03010"   "CEBPZOS"     "LINGO3"      "LINC02076"  
## [445] "EBF2"        "PLXNA4"      "ZNF880"      "POTEM"       "ADM5"        "MIR3659HG"  
## [451] "LINC01980"   "RUSC1-AS1"   "LINC01748"   "SOX21-AS1"   "MIR34AHG"    "ZBTB46-AS2" 
## [457] "PSMG3-AS1"   "TSPAN19"     "GOLGA8N"     "LNCTAM34A"   "HLA-B"       "DANT2"      
## [463] "GNAS-AS1"    "FAM88E"      "FOXD2-AS1"   "SHISA9"      "LINC00649"   "PCDHGC3"    
## [469] "NECTIN3-AS1" "PDE6B-AS1"   "SOX2-OT"     "ZNF512"      "PTCHD4"      "NEAT1"      
## [475] "LINC00682"   "SLCO5A1-AS1" "MIR4458HG"   "CASC9"       "LINC02972"   "PVT1"       
## [481] "GOLGA8K"     "AGA-DT"      "CHCHD10"     "YPEL3-DT"    "LINC00491"   "LINC02600"  
## [487] "LINC02315"   "FOXD1"       "ZFHX4-AS1"   "PCDHGA10"    "PCDHGB4"     "AP5B1"      
## [493] "SALL3"       "LINC02306"   "DIO3OS"      "LINC02301"   "LINC02820"   "TMEM179"    
## [499] "ZNF710-AS1"  "PWRN1"       "SPON1"       "LINC01896"   "PARD6G-AS1"  "KC6"        
## [505] "ZNF285"      "MAGEA2"      "CSAG3"       "MIA-RAB4B"   "ZNF470-DT"   "LINC01297"  
## [511] "TUBGCP5"

D50_HT:D50_AR

all_intersections$`D50_HT:D50_AR`
##   [1] "PRKAR2B"    "ITGA3"      "TAC1"       "SYT13"      "CPS1"       "TNFRSF1B"   "FLT4"      
##   [8] "CAMK2B"     "SEZ6"       "FGFR2"      "PRKCZ"      "ATP2B3"     "REEP1"      "RORA"      
##  [15] "LNX1"       "PPP2R2C"    "TRIP6"      "PUS7"       "MYH7"       "FKBP5"      "CACNA1I"   
##  [22] "GINS1"      "SALL4"      "SLC32A1"    "MAP1LC3A"   "NOL4"       "HSF4"       "CBLN1"     
##  [29] "ICAM5"      "PLA2G4C"    "PLEKHA4"    "ADAP1"      "CHN2"       "TFR2"       "RARRES2"   
##  [36] "EBF3"       "NEIL3"      "CRYAB"      "GMNN"       "ARFGEF3"    "HBEGF"      "GABRG2"    
##  [43] "HES1"       "SLC5A7"     "DNAJC6"     "PADI2"      "CA14"       "ATP10B"     "IQSEC3"    
##  [50] "MND1"       "SV2C"       "GRM4"       "PACSIN1"    "MIR9-1HG"   "OPRL1"      "BCL2L12"   
##  [57] "HIVEP3"     "TUBA4A"     "CDKN2D"     "EGLN3"      "CBFA2T3"    "GINS2"      "LIN28A"    
##  [64] "TRIM22"     "GPR12"      "MYBPH"      "ALDH1L2"    "GABBR2"     "ARHGEF39"   "PAK6"      
##  [71] "STRA6"      "CYP2C8"     "PCDH10"     "RASGEF1B"   "MTTP"       "RTN1"       "FBLN5"     
##  [78] "NOL3"       "RHBDL3"     "TAF4B"      "SLC16A3"    "CBLN2"      "SUSD4"      "ST6GAL2"   
##  [85] "SCN1A"      "CDCA7"      "MARCHF4"    "VWA5B2"     "OCIAD2"     "MARCHF1"    "SFRP2"     
##  [92] "PSD2"       "EML3"       "CNTN5"      "LYPD1"      "VEGFC"      "ADAMTS12"   "CCDC3"     
##  [99] "AKR1C2"     "STK32B"     "JAKMIP1"    "PID1"       "CDH12"      "GPR26"      "CNTNAP5"   
## [106] "GOLGA7B"    "PPP2R2B"    "SLC6A1"     "LDLRAP1"    "NPM2"       "CPAMD8"     "GPATCH4"   
## [113] "ALPL"       "GPX8"       "GPR85"      "MYORG"      "DIRAS2"     "LRFN5"      "AMER2"     
## [120] "RET"        "BTNL9"      "CDYL2"      "PRTG"       "YPEL4"      "LDLRAD4"    "NSG1"      
## [127] "FSTL5"      "B3GALNT1"   "KCNAB1"     "PROKR1"     "PCDH7"      "KCNK3"      "KCND3"     
## [134] "CDK5R2"     "CALB2"      "CKS1B"      "ABLIM3"     "IGDCC3"     "DPP10"      "CREG2"     
## [141] "CDK5R1"     "LY6H"       "FIBIN"      "DSCAML1"    "NHLH2"      "AURKB"      "FAM216B"   
## [148] "ARHGAP45"   "HHIPL1"     "CALN1"      "CHEK2"      "KCNQ3"      "PCDH9"      "POU6F1"    
## [155] "MAP7D2"     "ANKS1B"     "GPRIN3"     "PARPBP"     "SYN3"       "DLEU7"      "MYT1L"     
## [162] "MAPT"       "LUZP2"      "LIN28B"     "DIPK1C"     "DNER"       "JAKMIP3"    "INSYN2A"   
## [169] "RASSF10"    "PTPRT"      "SEMA4A"     "SLC6A9"     "SLC6A17"    "ADGRA1"     "DIO3"      
## [176] "NUP62CL"    "CACNA1E"    "HYLS1"      "TUSC1"      "SMOC1"      "PLXNB3"     "GRM3"      
## [183] "INF2"       "LINC02487"  "COL15A1"    "PCDHA7"     "MIR219A2HG" "C2orf74-DT" "SYT3"      
## [190] "LCNL1"      "SP9"        "INHBA-AS1"  "LINC02470"  "RFPL1S"     "LINC01503"  "LINC01322" 
## [197] "PCP4L1"     "EPHA5-AS1"  "PCDHGB7"    "TMPO-AS1"   "LINC01619"  "FIGNL2"     "GRIN2B"    
## [204] "EPOP"

D25_AR:D50_HT:D50_AR

all_intersections$`D25_AR:D50_HT:D50_AR`
## [1] "ZNF506"     "ZNF671"     "UNC5B"      "LRRC4C"     "GLT1D1"     "ZNF585B"    "ZNF790-AS1"

D25_HT:D25_AR:D50_AR

all_intersections$`D25_HT:D25_AR:D50_AR`
## NULL

D25_HT:D25_AR:D50_HT

all_intersections$`D25_HT:D25_AR:D50_HT`
##  [1] "CACNA1G"   "RSPO3"     "VAX1"      "ANGPT1"    "ZNF558"    "LRRN3"     "SOX11"    
##  [8] "PCDH18"    "SILC1"     "PURPL"     "LINC02381" "BLACAT1"

D25_HT:D50_HT:D50_AR

all_intersections$`D25_HT:D50_HT:D50_AR`
##  [1] "HECW1"      "CYP26B1"    "SYN1"       "ST3GAL1"    "MAMLD1"     "LRRC7"      "RIMBP2"    
##  [8] "GUCY1B1"    "ANKRD44"    "TRNT1"      "PCDHA6"     "SERTAD4"    "SLCO1A2"    "MLC1"      
## [15] "OLFM2"      "ACTA2"      "PTPN5"      "LAMA4"      "CHD5"       "NEK6"       "MSX2"      
## [22] "DNAJC15"    "CSMD2"      "MYRF"       "BCL11B"     "FOXP2"      "NFATC1"     "SH3BP5"    
## [29] "CTIF"       "PI15"       "MMRN1"      "NTRK3"      "CDH11"      "CACNA1A"    "RBMS3"     
## [36] "NKD2"       "LHFPL2"     "NFIB"       "FAM13C"     "ADM"        "CACNA1C"    "DAB2"      
## [43] "CA10"       "UNC5D"      "KIT"        "CACNA2D3"   "NRG2"       "CILP2"      "LMX1A"     
## [50] "KIF26B"     "INHBB"      "GUCY1A1"    "ZCCHC24"    "DACT1"      "CYYR1"      "RBFOX3"    
## [57] "FAM110B"    "PLEKHA2"    "NSG2"       "TNFRSF10D"  "UCP2"       "GRIN1"      "RNF182"    
## [64] "COL18A1"    "KCNH8"      "SEPTIN5"    "FAM183A"    "C3orf70"    "LITAF"      "MYT1"      
## [71] "TMEM229B"   "MMP17"      "GP1BB"      "NPTXR"      "CYP4F26P"   "FEZF1-AS1"  "ANKRD18B"  
## [78] "LINC01122"  "MIR210HG"   "PCDHA10"    "LINC02506"  "ZNF528-AS1" "ARHGAP23"   "COPG2IT1"

D25_HT:D25_AR:D50_HT:D50_AR

all_intersections$`D25_HT:D25_AR:D50_HT:D50_AR`
##  [1] "SPINK5"     "TRIM4"      "TMEM132D"   "IFTAP"      "ZNF667-AS1" "ZNF439"     "ZNF829"    
##  [8] "ZNF471"     "ZNF493"     "ZFP28"      "ZNF667"     "PCDHA2"     "MEG3"       "MEG9"      
## [15] "MEG8"       "LINC01515"  "PCDHA3"     "LINC02893"  "ZNF229"

Gene Ontology on genes shared by Day25 HT and Day50 AR

D25_HT_D50_AR_overlapGenes <- all_intersections$`D25_HT:D50_AR` #Genes in overlap

Universe <- union(rownames(DEAList_day25_HT$HT$res), rownames(DEAList_day50_AR$AR$res)) #Union of detected genes for universe

GeneVectors <- list()
GeneVectors$DEGenes <- ifelse(Universe %in% D25_HT_D50_AR_overlapGenes, 1, 0)
names(GeneVectors$DEGenes) <- Universe


BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors$DEGenes), 
                    mapping="org.Hs.eg.db", ID="symbol") %>% inverseList()

ResBP_D25_HT_D50_AR_overlapGenes <- topGOResults(Genes=GeneVectors$DEGenes, gene2GO=BPann, ontology='BP', geneSelectionFun = function(x) (x == 1),
                         desc=NULL, nodeSize=3, algorithm='weight01', statistic='fisher', 
                         EnTh=1, PvalTh=0.05, minTerms=12, geneTh=3,
                         saveRes=FALSE)
## Gene vector contains levels:
## 
## Building most specific GOs .....
##  ( 11898 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 15542 GO terms and 35379 relations. )
## 
## Annotating nodes ...............
##  ( 14387 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1335 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  10 nodes to be scored   (31 eliminated genes)
## 
##   Level 14:  11 nodes to be scored   (101 eliminated genes)
## 
##   Level 13:  21 nodes to be scored   (230 eliminated genes)
## 
##   Level 12:  38 nodes to be scored   (452 eliminated genes)
## 
##   Level 11:  58 nodes to be scored   (1630 eliminated genes)
## 
##   Level 10:  99 nodes to be scored   (3681 eliminated genes)
## 
##   Level 9:   135 nodes to be scored  (4772 eliminated genes)
## 
##   Level 8:   171 nodes to be scored  (5819 eliminated genes)
## 
##   Level 7:   207 nodes to be scored  (7440 eliminated genes)
## 
##   Level 6:   217 nodes to be scored  (9962 eliminated genes)
## 
##   Level 5:   181 nodes to be scored  (11772 eliminated genes)
## 
##   Level 4:   105 nodes to be scored  (13190 eliminated genes)
## 
##   Level 3:   55 nodes to be scored   (13917 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (14137 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (14190 eliminated genes)
custom_theme <- theme(
  panel.background = element_blank(),  # No background color
  panel.border = element_rect(color = "black", fill = NA, size = 0.5),  # Black border around panels
  panel.grid.major = element_line(color = "grey90", size = 0.5),  # Grey major grid lines
  panel.grid.minor = element_blank(),  # No minor grid lines
  axis.text = element_text(color = "black"),  # Black text for axis labels
  axis.title = element_text(color = "black"),  # Black text for axis titles
  plot.title = element_text(color = "black", hjust = 0.5),  # Black plot title, centered
  legend.position = "top",  # No legend
  strip.background = element_blank(),  # No background for facet labels
  strip.text = element_text(color = "black", face = "bold")  # Black, bold text for facet labels
)
## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
ResOrdered <- ResBP_D25_HT_D50_AR_overlapGenes$ResSel
ResOrdered <- ResOrdered[order(ResOrdered$Statistics, decreasing = TRUE), ]
MaxVal <- round(max(-log10(as.numeric(ResOrdered$Statistics)), na.rm=TRUE), 0) +1
ResOrdered$fillcolor <- '#ed72a9'# '#31688EFF'
ResOrdered$Term <- factor(ResOrdered$Term, levels = ResOrdered$Term)

ResOrdered <- ResOrdered %>% filter(ResOrdered$Statistics < 0.05)

ggplot(data=ResOrdered, aes(x=Term, y=-log10(as.numeric(Statistics)), size=ER)) + 
    geom_hline(yintercept=-log10(0.05), col='gray80', lty='longdash') +
    geom_point(stat='identity', colour="black", pch=21, fill=ResOrdered$fillcolor) +
    #geom_text(aes(y=0), label=ResOrdered$Term, hjust=0, size=4, color='black') + 
    scale_y_continuous(breaks=seq(0,MaxVal,2), labels=abs(seq(0, MaxVal, 2)), limits=c(0,MaxVal), expand=c(0.025, 0.025)) +
    ylab('-log10 PValue') + xlab('') +
    theme_bw() +
    labs(size='Enrichment Ratio') +
    theme(legend.position='right', axis.text = element_text(colour = 'black', size=12), 
          plot.title= element_text(face='', size=10, hjust = 0.5)) +
    custom_theme +
    scale_x_discrete(position = "top") +
    coord_flip()

ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'GO_BP_sharedGenes_D25HTandD50AR.pdf'), device = 'pdf', width = 8, height = 4)

Gene Ontology on genes in Day25 HT and Day50 Overlap with SFARI genes

D25_HT_D50_AR_overlapGenesSFARI <- rownames(CompareResFlip$Significant)
GeneVectors$DEGenesSFARI <- ifelse(Universe %in% D25_HT_D50_AR_overlapGenesSFARI, 1, 0)
names(GeneVectors$DEGenesSFARI) <- Universe


ResBP_D25_HT_D50_AR_overlapGenesSFARI <- topGOResults(Genes=GeneVectors$DEGenesSFARI, gene2GO=BPann, ontology='BP', geneSelectionFun = function(x) (x == 1),
                         desc=NULL, nodeSize=1, algorithm='weight01', statistic='fisher', 
                         EnTh=1, PvalTh=0.05, minTerms=12, geneTh=1,
                         saveRes=FALSE)
## Gene vector contains levels:
## 
## Building most specific GOs .....
##  ( 11898 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 15542 GO terms and 35379 relations. )
## 
## Annotating nodes ...............
##  ( 14387 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 0 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed - there are no feasible
## GO terms!
## No GO category enriched

sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
##  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
## [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] gplots_3.1.3                ggvenn_0.1.10               scales_1.3.0               
##  [4] DESeq2_1.34.0               colorRamp2_0.1.0            ComplexHeatmap_2.10.0      
##  [7] UpSetR_1.4.0                GeneOverlap_1.30.0          data.table_1.14.2          
## [10] cowplot_1.1.1               RColorBrewer_1.1-3          gridExtra_2.3              
## [13] sechm_1.2.0                 topGO_2.46.0                SparseM_1.81               
## [16] GO.db_3.14.0                graph_1.72.0                org.Hs.eg.db_3.14.0        
## [19] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
## [22] MatrixGenerics_1.6.0        matrixStats_0.62.0          RNASeqBulkExploratory_0.2.1
## [25] overlapper_0.99.1           tidyr_1.2.0                 dplyr_1.0.9                
## [28] forcats_0.5.2               viridis_0.6.2               viridisLite_0.4.1          
## [31] enrichplot_1.14.2           ggplot2_3.5.1               AnnotationDbi_1.56.2       
## [34] IRanges_2.28.0              S4Vectors_0.32.4            Biobase_2.54.0             
## [37] BiocGenerics_0.40.0         clusterProfiler_4.2.2      
## 
## loaded via a namespace (and not attached):
##   [1] shinydashboard_0.7.2     utf8_1.2.2               tidyselect_1.2.0        
##   [4] RSQLite_2.2.12           htmlwidgets_1.5.4        TSP_1.2-1               
##   [7] BiocParallel_1.28.3      Rtsne_0.16               scatterpie_0.1.7        
##  [10] munsell_0.5.0            codetools_0.2-18         DT_0.25                 
##  [13] withr_2.5.0              colorspace_2.0-3         GOSemSim_2.20.0         
##  [16] filelock_1.0.2           highr_0.9                knitr_1.40              
##  [19] rstudioapi_0.14          DOSE_3.20.1              labeling_0.4.2          
##  [22] GenomeInfoDbData_1.2.7   polyclip_1.10-0          bit64_4.0.5             
##  [25] farver_2.1.1             downloader_0.4           vctrs_0.6.5             
##  [28] treeio_1.18.1            generics_0.1.3           lambda.r_1.2.4          
##  [31] xfun_0.31                BiocFileCache_2.2.1      R6_2.5.1                
##  [34] doParallel_1.0.17        clue_0.3-61              graphlayouts_0.8.2      
##  [37] seriation_1.3.6          locfit_1.5-9.6           bitops_1.0-7            
##  [40] cachem_1.0.6             fgsea_1.20.0             gridGraphics_0.5-1      
##  [43] DelayedArray_0.20.0      assertthat_0.2.1         shinycssloaders_1.0.0   
##  [46] promises_1.2.0.1         BiocIO_1.4.0             ggraph_2.0.5            
##  [49] gtable_0.3.1             tidygraph_1.2.1          rlang_1.1.4             
##  [52] genefilter_1.76.0        GlobalOptions_0.1.2      splines_4.1.1           
##  [55] rtracklayer_1.54.0       lazyeval_0.2.2           yaml_2.3.5              
##  [58] reshape2_1.4.4           GenomicFeatures_1.46.5   crosstalk_1.2.0         
##  [61] httpuv_1.6.6             qvalue_2.26.0            tools_4.1.1             
##  [64] ggplotify_0.1.0          ellipsis_0.3.2           jquerylib_0.1.4         
##  [67] Rcpp_1.0.9               plyr_1.8.7               progress_1.2.2          
##  [70] zlibbioc_1.40.0          purrr_0.3.5              RCurl_1.98-1.7          
##  [73] prettyunits_1.1.1        GetoptLong_1.0.5         ggrepel_0.9.1           
##  [76] cluster_2.1.2            tinytex_0.42             magrittr_2.0.3          
##  [79] futile.options_1.0.1     DO.db_2.9                circlize_0.4.15         
##  [82] randomcoloR_1.1.0.1      mime_0.12                hms_1.1.2               
##  [85] patchwork_1.3.0          evaluate_0.17            xtable_1.8-4            
##  [88] XML_3.99-0.10            VennDiagram_1.7.3        shape_1.4.6             
##  [91] compiler_4.1.1           biomaRt_2.50.3           tibble_3.1.7            
##  [94] KernSmooth_2.23-20       V8_4.2.0                 crayon_1.4.1            
##  [97] shadowtext_0.1.2         htmltools_0.5.2          later_1.3.0             
## [100] ggfun_0.0.7              geneplotter_1.72.0       aplot_0.1.8             
## [103] DBI_1.1.3                formatR_1.12             tweenr_2.0.2            
## [106] dbplyr_2.2.0             MASS_7.3-54              rappdirs_0.3.3          
## [109] Matrix_1.3-4             cli_3.6.3                parallel_4.1.1          
## [112] igraph_1.3.5             pkgconfig_2.0.3          registry_0.5-1          
## [115] GenomicAlignments_1.30.0 plotly_4.10.4            xml2_1.3.3              
## [118] foreach_1.5.2            ggtree_3.2.1             annotate_1.72.0         
## [121] bslib_0.4.0              XVector_0.34.0           yulab.utils_0.0.5       
## [124] stringr_1.4.1            digest_0.6.28            Biostrings_2.62.0       
## [127] rmarkdown_2.17           fastmatch_1.1-3          tidytree_0.3.9          
## [130] restfulr_0.0.15          curl_4.3.3               gtools_3.9.4            
## [133] shiny_1.7.2              Rsamtools_2.10.0         rjson_0.2.21            
## [136] lifecycle_1.0.3          nlme_3.1-152             jsonlite_1.7.2          
## [139] futile.logger_1.4.3      fansi_0.5.0              pillar_1.8.1            
## [142] ggsci_3.0.0              lattice_0.20-45          KEGGREST_1.34.0         
## [145] fastmap_1.1.0            httr_1.4.4               survival_3.2-13         
## [148] glue_1.6.2               png_0.1-7                iterators_1.0.14        
## [151] bit_4.0.4                ggforce_0.4.1            stringi_1.7.8           
## [154] sass_0.4.2               blob_1.2.3               caTools_1.18.2          
## [157] memoise_2.0.1            ape_5.6-2

last update on: Mon Jan 13 10:17:20 2025